59 lines
1.9 KiB
R
59 lines
1.9 KiB
R
#!/usr/bin/env Rscript
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#########################################################
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# TASK: To calculate Allele Frequency and
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# Odds Ratio from master data
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#########################################################
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# load libraries
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#source("Header_TT.R")
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require("getopt", quietly = TRUE) # cmd parse arguments
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/functions/")
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getwd()
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# load functions
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source("plotting_globals.R")
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source("mychisq_or.R")
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source("myaf_or_calcs.R")
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# cmd options + sensible defaults
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drug = "streptomycin"
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gene = "gid"
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# call function
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import_dirs(drug, gene)
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# input file 1: master data
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#in_filename_master = 'original_tanushree_data_v2.csv' #19K
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in_filename_master = 'mtb_gwas_meta_v6.csv' #35k
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infile_master = paste0(datadir, in_filename_master)
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cat(paste0('Reading infile1: raw data', ' ', infile_master) )
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# input file 2: gene associated meta data file to extract valid snps and add calcs to.
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# This is outfile_metadata from data_extraction.py
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in_filename_metadata = paste0(tolower(gene), '_metadata.csv')
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infile_metadata = paste0(outdir, '/', in_filename_metadata)
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cat(paste0('Reading input file 2 i.e gene associated metadata:', infile_metadata))
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# out_filename_af_or = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
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out_filename_af_or = paste0(tolower(gene), '_af_or.csv')
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outfile_af_or = paste0(outdir, '/', out_filename_af_or)
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cat(paste0('Output file with full path:', outfile_af_or))
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cat("master data:", infile_master)
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cat("gene data:", infile_metadata)
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dr_muts_col # comes from global (dr_mutations_<drug>)
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other_muts_col # comes from global (other_mutations_<drug>)
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#################################################
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my_afor ( infile_master
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, infile_metadata
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, outfile = outfile_af_or
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#, outfile = "FOO_TEST.csv"
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, drug
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, gene
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, idcol = "id"
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, dr_muts_col
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, other_muts_col
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)
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