372 lines
No EOL
12 KiB
R
372 lines
No EOL
12 KiB
R
#!/usr/bin/env Rscript
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#########################################################
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# TASK: To combine struct params and meta data for plotting
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# Input csv files:
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# 1) <gene>_all_params.csv
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# 2) <gene>_meta_data.csv
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# Output:
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# 1) muts with opposite effects on stability
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# 2) large combined df including NAs for AF, OR,etc
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# Dim: same no. of rows as gene associated meta_data_with_AFandOR
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# 3) small combined df including NAs for AF, OR, etc.
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# Dim: same as mcsm data
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# 4) large combined df excluding NAs
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# Dim: dim(#1) - na_count_df2
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# 5) small combined df excluding NAs
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# Dim: dim(#2) - na_count_df3
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# This script is sourced from other .R scripts for plotting
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#########################################################
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#=======================================================================
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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getwd()
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source("Header_TT.R")
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#require(data.table)
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#require(arsenal)
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#require(compare)
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#library(tidyverse)
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source("plotting_data.R")
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# should return the following dfs, directories and variables
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# my_df
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# my_df_u
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# my_df_u_lig
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# dup_muts
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cat(paste0("Directories imported:"
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, "\ndatadir:", datadir
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, "\nindir:", indir
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, "\noutdir:", outdir
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, "\nplotdir:", plotdir))
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cat(paste0("Variables imported:"
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, "\ndrug:", drug
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, "\ngene:", gene
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, "\ngene_match:", gene_match
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, "\nLength of upos:", length(upos)
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, "\nAngstrom symbol:", angstroms_symbol))
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# clear excess variable
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rm(my_df, upos, dup_muts)
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#========================================================
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#===========
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# input
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#===========
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#in_file1: output of plotting_data.R
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# my_df_u
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# quick checks
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head(my_df_u[, c("mutation", "mutation2")])
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cols_to_extract = c("mutationinformation", "mutation", "or_mychisq", "or_kin", "af", "af_kin")
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foo = my_df_u[, colnames(my_df_u)%in% cols_to_extract]
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which(is.na(my_df_u$af_kin)) == which(is.na(my_df_u$af))
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baz = cbind(my_df_u$mutation, my_df_u$or_mychisq, bar$mutation, bar$or_mychisq)
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colnames(baz) = c("my_df_u_muts", "my_df_u_or", "real_muts", "real_or")
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# infile 2: gene associated meta data
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#in_filename_gene_metadata = paste0(tolower(gene), "_meta_data_with_AFandOR.csv")
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in_filename_gene_metadata = paste0(tolower(gene), "_metadata.csv")
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infile_gene_metadata = paste0(outdir, "/", in_filename_gene_metadata)
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cat(paste0("Input infile 2:", infile_gene_metadata))
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#===========
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# output
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#===========
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# other variables that you can write
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# primarily called by other scripts for plotting
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# PS combined:
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# 1) merged_df2
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# 2) merged_df2_comp
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# 3) merged_df3
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# 4) merged_df3_comp
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# LIG combined:
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# 5) merged_df2_lig
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# 6) merged_df2_comp_lig
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# 7) merged_df3_lig
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# 8) merged_df3_comp_lig
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#%%===============================================================
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###########################
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# 2: Read file: <gene>_meta data.csv
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###########################
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cat("Reading meta data file:", infile_gene_metadata)
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gene_metadata <- read.csv(infile_gene_metadata
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, stringsAsFactors = F
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, header = T)
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cat("Dim:", dim(gene_metadata))
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# counting NAs in AF, OR cols:
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if (identical(sum(is.na(my_df_u$or_mychisq))
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, sum(is.na(my_df_u$pval_fisher))
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, sum(is.na(my_df_u$af)))){
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cat("\nPASS: NA count match for OR, pvalue and AF\n")
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na_count = sum(is.na(my_df_u$af))
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cat("\nNo. of NAs: ", sum(is.na(my_df_u$or_mychisq)))
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} else{
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cat("\nFAIL: NA count mismatch"
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, "\nNA in OR: ", sum(is.na(my_df_u$or_mychisq))
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, "\nNA in pvalue: ", sum(is.na(my_df_u$pval_fisher))
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, "\nNA in AF:", sum(is.na(my_df_u$af)))
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}
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if (identical(sum(is.na(my_df_u$or_kin))
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, sum(is.na(my_df_u$pwald_kin))
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, sum(is.na(my_df_u$af_kin)))){
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cat("\nPASS: NA count match for OR, pvalue and AF\n from Kinship matrix calculations")
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na_count = sum(is.na(my_df_u$af_kin))
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cat("\nNo. of NAs: ", sum(is.na(my_df_u$or_kin)))
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} else{
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cat("\nFAIL: NA count mismatch"
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, "\nNA in OR: ", sum(is.na(my_df_u$or_kin))
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, "\nNA in pvalue: ", sum(is.na(my_df_u$pwald_kin))
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, "\nNA in AF:", sum(is.na(my_df_u$af_kin)))
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}
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str(gene_metadata)
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###################################################################
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# combining: PS
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###################################################################
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# sort by position (same as my_df)
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head(gene_metadata$position)
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gene_metadata = gene_metadata[order(gene_metadata$position),]
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head(gene_metadata$position)
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#=========================
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# Merge 1: merged_df2
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# dfs with NAs in ORs
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#=========================
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head(my_df_u$mutationinformation)
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head(gene_metadata$mutationinformation)
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# Find common columns b/w two df
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merging_cols = intersect(colnames(my_df_u), colnames(gene_metadata))
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cat(paste0("Merging dfs with NAs: big df (1-many relationship b/w id & mut)"
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, "\nNo. of merging cols:", length(merging_cols)
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, "\nMerging columns identified:"))
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print(merging_cols)
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# important checks!
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table(nchar(my_df_u$mutationinformation))
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table(nchar(my_df_u$wild_type))
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table(nchar(my_df_u$mutant_type))
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table(nchar(my_df_u$position))
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# all.y because x might contain non-structural positions!
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merged_df2 = merge(x = gene_metadata
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, y = my_df_u
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, by = merging_cols
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, all.y = T)
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cat("Dim of merged_df2: ", dim(merged_df2))
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head(merged_df2$position)
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# sanity check
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cat("Checking nrows in merged_df2")
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if(nrow(gene_metadata) == nrow(merged_df2)){
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cat("PASS: nrow(merged_df2) = nrow (gene associated gene_metadata)"
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,"\nExpected no. of rows: ",nrow(gene_metadata)
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,"\nGot no. of rows: ", nrow(merged_df2))
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} else{
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cat("FAIL: nrow(merged_df2)!= nrow(gene associated gene_metadata)"
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, "\nExpected no. of rows after merge: ", nrow(gene_metadata)
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, "\nGot no. of rows: ", nrow(merged_df2)
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, "\nFinding discrepancy")
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merged_muts_u = unique(merged_df2$mutationinformation)
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meta_muts_u = unique(gene_metadata$mutationinformation)
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# find the index where it differs
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unique(meta_muts_u[! meta_muts_u %in% merged_muts_u])
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quit()
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}
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#=========================
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# Merge 2: merged_df3
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# dfs with NAs in ORs
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#
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# Cannot trust lineage, country from this df as the same mutation
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# can have many different lineages
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# but this should be good for the numerical corr plots
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#=========================
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# remove duplicated mutations
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cat("Merging dfs without NAs: small df (removing muts with no AF|OR associated)"
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,"\nCannot trust lineage info from this"
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,"\nlinking col: mutationinforamtion"
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,"\nfilename: merged_df3")
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merged_df3 = merged_df2[!duplicated(merged_df2$mutationinformation),]
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head(merged_df3$position); tail(merged_df3$position) # should be sorted
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# sanity check
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cat("Checking nrows in merged_df3")
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if(nrow(my_df_u) == nrow(merged_df3)){
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cat("PASS: No. of rows match with my_df"
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,"\nExpected no. of rows: ", nrow(my_df_u)
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,"\nGot no. of rows: ", nrow(merged_df3))
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} else {
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cat("FAIL: No. of rows mismatch"
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, "\nNo. of rows my_df: ", nrow(my_df_u)
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, "\nNo. of rows merged_df3: ", nrow(merged_df3))
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quit()
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}
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# counting NAs in AF, OR cols in merged_df3
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# this is because mcsm has no AF, OR cols,
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# so you cannot count NAs
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if (identical(sum(is.na(merged_df3$or_kin))
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, sum(is.na(merged_df3$pwald_kin))
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, sum(is.na(merged_df3$af_kin)))){
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cat("PASS: NA count match for OR, pvalue and AF\n")
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na_count_df3 = sum(is.na(merged_df3$af_kin))
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cat("No. of NAs: ", sum(is.na(merged_df3$or_kin)))
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} else{
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cat("FAIL: NA count mismatch"
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, "\nNA in OR: ", sum(is.na(merged_df3$or_kin))
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, "\nNA in pvalue: ", sum(is.na(merged_df3$pwald_kin))
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, "\nNA in AF:", sum(is.na(merged_df3$af_kin)))
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}
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# check if the same or and afs are missing for
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if ( identical( which(is.na(merged_df2$or_mychisq)), which(is.na(merged_df2$or_kin)))
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&& identical( which(is.na(merged_df2$af)), which(is.na(merged_df2$af_kin)))
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&& identical( which(is.na(merged_df2$pval_fisher)), which(is.na(merged_df2$pwald_kin))) ){
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cat("PASS: Indices match for mychisq and kin ors missing values")
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} else{
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cat("Index mismatch: mychisq and kin ors missing indices match")
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quit()
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}
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#=========================
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# Merge3: merged_df2_comp
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# same as merge 1 but excluding NAs from ORs, etc.
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#=========================
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cat("Merging dfs without any NAs: big df (1-many relationship b/w id & mut)"
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,"\nlinking col: Mutationinforamtion"
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,"\nfilename: merged_df2_comp")
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if ( identical( which(is.na(merged_df2$af)), which(is.na(merged_df2$af_kin))) ){
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print("mychisq and kin ors missing indices match. Procedding with omitting NAs")
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na_count_df2 = sum(is.na(merged_df2$af))
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merged_df2_comp = merged_df2[!is.na(merged_df2$af),]
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# sanity check: no +-1 gymnastics
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cat("Checking nrows in merged_df2_comp")
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if(nrow(merged_df2_comp) == (nrow(merged_df2) - na_count_df2)){
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cat("\nPASS: No. of rows match"
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,"\nDim of merged_df2_comp: "
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,"\nExpected no. of rows: ", nrow(merged_df2) - na_count_df2
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, "\nNo. of rows: ", nrow(merged_df2_comp)
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, "\nNo. of cols: ", ncol(merged_df2_comp))
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}else{
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cat("FAIL: No. of rows mismatch"
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,"\nExpected no. of rows: ", nrow(merged_df2) - na_count_df2
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,"\nGot no. of rows: ", nrow(merged_df2_comp))
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}
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}else{
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print("Index mismatch for mychisq and kin ors. Aborting NA ommission")
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}
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#=========================
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# Merge4: merged_df3_comp
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# same as merge 2 but excluding NAs from ORs, etc or
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# remove duplicate mutation information
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#=========================
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if ( identical( which(is.na(merged_df3$af)), which(is.na(merged_df3$af_kin))) ){
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print("mychisq and kin ors missing indices match. Procedding with omitting NAs")
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na_count_df3 = sum(is.na(merged_df3$af))
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#merged_df3_comp = merged_df3_comp[!duplicated(merged_df3_comp$mutationinformation),] # a way
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merged_df3_comp = merged_df3[!is.na(merged_df3$af),] # another way
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cat("Checking nrows in merged_df3_comp")
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if(nrow(merged_df3_comp) == (nrow(merged_df3) - na_count_df3)){
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cat("\nPASS: No. of rows match"
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,"\nDim of merged_df3_comp: "
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,"\nExpected no. of rows: ", nrow(merged_df3) - na_count_df3
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, "\nNo. of rows: ", nrow(merged_df3_comp)
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, "\nNo. of cols: ", ncol(merged_df3_comp))
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}else{
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cat("FAIL: No. of rows mismatch"
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,"\nExpected no. of rows: ", nrow(merged_df3) - na_count_df3
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,"\nGot no. of rows: ", nrow(merged_df3_comp))
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}
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} else{
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print("Index mismatch for mychisq and kin ors. Aborting NA ommission")
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}
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# alternate way of deriving merged_df3_comp
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foo = merged_df3[!is.na(merged_df3$af),]
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bar = merged_df3_comp[!duplicated(merged_df3_comp$mutationinformation),]
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# compare dfs: foo and merged_df3_com
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all.equal(foo, bar)
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#summary(comparedf(foo, bar))
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#==============================================================
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#################
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# OPTIONAL: write ALL 4 output files
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#################
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#outvars = c("merged_df2"
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# , "merged_df3"
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# , "merged_df2_comp"
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# , "merged_df3_comp")
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#cat("Writing output files: "
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# , "\nPath:", outdir)
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#for (i in outvars){
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# out_filename = paste0(i, ".csv")
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# outfile = paste0(outdir, "/", out_filename)
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# cat("Writing output file:"
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# ,"\nFilename: ", out_filename,"\n")
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# write.csv(get(i), outfile, row.names = FALSE)
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# cat("Finished writing: ", outfile
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# , "\nNo. of rows: ", nrow(get(i))
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# , "\nNo. of cols: ", ncol(get(i)), "\n")
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#}
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#*************************
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# clear variables
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rm(foo, bar, gene_metadata
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, in_filename_params, infile_params, merging_cols
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, in_filename_gene_metadata, infile_gene_metadata
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, merged_df2v2, merged_df2v3)
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#*************************
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#####################################################################
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# Combining: LIG
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#####################################################################
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#=========================
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# Merges 5-8
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#=========================
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merged_df2_lig = merged_df2[merged_df2$ligand_distance<10,]
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merged_df2_comp_lig = merged_df2_comp[merged_df2_comp$ligand_distance<10,]
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merged_df3_lig = merged_df3[merged_df3$ligand_distance<10,]
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merged_df3_comp_lig = merged_df3_comp[merged_df3_comp$ligand_distance<10,]
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# sanity check
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if (nrow(merged_df3_lig) == nrow(my_df_u_lig)){
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print("PASS: verified merged_df3_lig")
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}else{
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cat(paste0("FAIL: nrow mismatch for merged_df3_lig"
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, "\nExpected:", nrow(my_df_u_lig)
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, "\nGot:", nrow(merged_df3_lig)))
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}
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#==========================================================================
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# end of script
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##========================================================================== |