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Commit 9feb8682 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
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Edit and clean up R scripts

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src/IMP_visualize_MG.R
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src/IMP_visualize_MGMT.R
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......@@ -41,22 +41,6 @@ GC.dat_file <- args[12]
coords_file <- args[13]
annot_file <- args[14]
# Only for testing purposes
# out_dir <- "/scratch/users/snarayanasamy/A02_20141212/MGMT/results/"
# MG.read.count_file <- "/scratch/users/snarayanasamy/A02_20141212/MG/MG.read_counts.txt"
# MT.read.count_file <- "/scratch/users/snarayanasamy/A02_20141212/MT/MT.read_counts.txt"
# MG.map.summary_file <- "/scratch/users/snarayanasamy/A02_20141212/MG/MG.assembly.merged.coverage_flagstat.txt"
# MT.map.summary_file <- "/scratch/users/snarayanasamy/A02_20141212/MT/MT.assembly.merged.coverage_flagstat.txt"
# MG.cov_file <- "/scratch/users/snarayanasamy/A02_20141212/MG/MG.assembly.merged.coverage_coverage.txt"
# MT.cov_file <- "/scratch/users/snarayanasamy/A02_20141212/MT/MT.assembly.merged.coverage_coverage.txt"
# MG.depth_file <- "/scratch/users/snarayanasamy/A02_20141212/MG/MG.assembly.merged.coverage_depth.txt"
# MT.depth_file <- "/scratch/users/snarayanasamy/A02_20141212/MT/MT.assembly.merged.coverage_depth.txt"
# MG.var_file <- "/scratch/users/snarayanasamy/A02_20141212/MG/MG.variants.isec.vcf.gz"
# MT.var_file <- "/scratch/users/snarayanasamy/A02_20141212/MT/MT.variants.isec.vcf.gz"
# GC.dat_file <- "/scratch/users/snarayanasamy/A02_20141212/MGMT/MGMT.assembly.merged.gc_content.txt"
# coords_file <- "/scratch/users/snarayanasamy/A02_20141212/MGMT/MGMT.vizbin.points_annot"
# annot_file <- "/scratch/users/snarayanasamy/A02_20141212/MGMT/annotation/annotation.filt.gff"
###################################################################################################
## Initialize functions for various calculations and normalizations
###################################################################################################
......@@ -999,7 +983,7 @@ theme_black()
dev.off()
## Save the R workspace
save.image(name_plot("results.Rdat"))
save.image(name_plot("MGMT_results.Rdat"))
## Beanplot function
src/IMP_visualize_MT.R
+ 55
− 590
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