-
Notifications
You must be signed in to change notification settings - Fork 2
/
SequenzaPreProcess_v2.2.R
executable file
·53 lines (42 loc) · 1.72 KB
/
SequenzaPreProcess_v2.2.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
library(sequenza)
library(optparse)
## For now, test if commands are in original, trailing format, or new opt-parse format
option_list = list(
make_option(c("-s", "--snp_file"), type="character", default=NULL,
help="varscan snp file name", metavar="character"),
make_option(c("-c", "--cnv_file"), type="character", default=NULL,
help="varscan copy number file name [default= %default]", metavar="character"),
make_option(c("-y", "--remove_Y_vars"), type="logical", default=TRUE,
help="Remove Y chromosome variants? [default= %default]", metavar="logical"),
make_option(c("-p", "--prefix"), type="character", default=NULL,
help="Output prefix for processed data file [default= %default]", metavar="character")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
snp.file <- opt$snp_file
cnv.file <- opt$cnv_file
remove_Y <- opt$remove_Y_vars
prefix <- opt$prefix
print("Getting SeqZ file for Sequenza:")
########
# MAIN #
########
## read the snp and cnv files
snp <- read.table(snp.file,sep="\t",header = TRUE)
cnv <- read.table(cnv.file,sep="\t",header = TRUE)
## remove chromosome M because it seems to cause problems
snp <-subset(snp,chrom!="chrM")
cnv <-subset(cnv,chrom!="chrM")
## remove chromosome Y because it seems to cause problems
if(remove_Y){
snp<-subset(snp,chrom!="chrY")
cnv<-subset(cnv,chrom!="chrY")
}
##### Adjust for filtered data, if needed
cnv<-cnv[,1:8]
colnames(cnv)[7]="log2_ratio"
##### prepare sequenza data file
seqz.data <- VarScan2seqz(varscan.somatic = snp,
varscan.copynumber = cnv)
file <- paste0(prefix, ".seqz")
write.table(seqz.data, file, col.names = TRUE, row.names = FALSE, sep = "\t")