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changed filename to the new combined output (mcsm+struct params)

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This commit is contained in:
Tanushree Tunstall 2020-03-27 12:43:48 +00:00
parent 82e96fcdba
commit d1da203df0
2 changed files with 9 additions and 3 deletions
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5
mcsm_analysis/pyrazinamide/scripts/combining_two_df.R
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@ -1,7 +1,7 @@
######################################################### #########################################################
# TASK: To combine mcsm and meta data with af and or files # TASK: To combine mcsm and meta data with af and or files
# Input csv files: # Input csv files:
# 1) mcsm output formatted # 1) mcsm normalised and struct params
# 2) gene associated meta_data_with_AFandOR # 2) gene associated meta_data_with_AFandOR
# Output: # Output:
@ -50,7 +50,8 @@ datadir = paste0('~/git/Data')
# infile1: mCSM data # infile1: mCSM data
#indir = '~/git/Data/pyrazinamide/input/processed/' #indir = '~/git/Data/pyrazinamide/input/processed/'
indir = paste0(datadir, '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline} indir = paste0(datadir, '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
in_filename = 'mcsm_complex1_normalised.csv' #in_filename = 'mcsm_complex1_normalised.csv'
in_filename = 'pnca_mcsm_struct_params.csv'
infile = paste0(indir, '/', in_filename) infile = paste0(indir, '/', in_filename)
cat(paste0('Reading infile1: mCSM output file', ' ', infile) ) cat(paste0('Reading infile1: mCSM output file', ' ', infile) )

7
mcsm_analysis/pyrazinamide/scripts/combining_two_df_lig.R
View file

@ -3,6 +3,10 @@
# by filtering for distance to ligand (<10Ang). # by filtering for distance to ligand (<10Ang).
# This script doesn't output anything. # This script doesn't output anything.
# This script is sourced from other .R scripts for plotting ligand plots # This script is sourced from other .R scripts for plotting ligand plots
# Input csv files:
# 1) mcsm normalised and struct params
# 2) gene associated meta_data_with_AFandOR
######################################################### #########################################################
getwd() getwd()
setwd('~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/') setwd('~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/')
@ -35,7 +39,8 @@ cat(gene_match)
# infile1: mCSM data # infile1: mCSM data
#indir = '~/git/Data/pyrazinamide/input/processed/' #indir = '~/git/Data/pyrazinamide/input/processed/'
indir = paste0('~/git/Data', '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline} indir = paste0('~/git/Data', '/', drug, '/', 'output') # revised {TODO: change in mcsm pipeline}
in_filename = 'mcsm_complex1_normalised.csv' #in_filename = 'mcsm_complex1_normalised.csv'
in_filename = 'pnca_mcsm_struct_params.csv'
infile = paste0(indir, '/', in_filename) infile = paste0(indir, '/', in_filename)
cat(paste0('Reading infile1: mCSM output file', ' ', infile) ) cat(paste0('Reading infile1: mCSM output file', ' ', infile) )