Mercurial > repos > jeremyjliu > region_motif_enrichment
diff region_motif_compare.r @ 31:0e031bf8c5b1 draft
Uploaded
| author | jeremyjliu |
|---|---|
| date | Wed, 04 Feb 2015 13:52:22 -0500 |
| parents | 4439b2ed86e9 |
| children | 9525574f700f |
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--- a/region_motif_compare.r Mon Jan 05 22:28:37 2015 -0500 +++ b/region_motif_compare.r Wed Feb 04 13:52:22 2015 -0500 @@ -4,7 +4,7 @@ # corrections. All enrichment ratios relative to overall count / gc ratios. # Author: Jeremy liu # Email: jeremy.liu@yale.edu -# Date: 14/07/03 +# Date: 15/02/04 # Note: This script is meant to be invoked with the following command # R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <db> <intab1> <intab2> # <enriched_tab> <depleted_tab> <plots_png> @@ -24,20 +24,19 @@ # Set common and data directories args <- commandArgs() workingDir = args[7] -dbDir = concat(workingDir, "/region_motif_db") dbCode = args[8] # dbCode "c" implemented when pwmFile is loaded if (dbCode == "t" | dbCode == "p") { - pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData") + pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData") } else if (dbCode == "j") { - pwmFile = concat(dbDir, "/pwms/jaspar.jolma.pwms.from.seq.RData") + pwmFile = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData") } else if (dbCode == "m") { - pwmFile = concat(dbDir, "/pwms/mm9.pwms.from.seq.RData") + pwmFile = concat(workingDir, "/pwms/mm9.pwms.from.seq.RData") } else if (dbCode == "c") { # rest of dbCode "c" implemeted when pwmFile loaded - pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData") - pwmFile2 = concat(dbDir, "/pwms/jaspar.jolma.pwms.from.seq.RData") + pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData") + pwmFile2 = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData") } else { - pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData") + pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData") } # Set input and reference files @@ -48,7 +47,7 @@ plotsPng = args[13] # Load dependencies -source(concat(workingDir, "/region_motif_lib/plotting.r")) +source(concat(workingDir, "/plotting.r")) # Auxiliary function to read in tab file and prepare the data read_tsv <- function(file) {