aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorDanny Arends2020-04-29 04:38:42 -0500
committerDanny Arends2020-04-29 04:38:42 -0500
commit10b8dc7af35f0d221daf121d0e3c0a52d9223368 (patch)
treedc29a22d162cd827ea689dfbed0870b282ff97ac
parent86d885f5f2e1069a5b1606296a71992805486aec (diff)
downloadgenenetwork2-10b8dc7af35f0d221daf121d0e3c0a52d9223368.tar.gz
Fixing loading of the ITP data as a 4way cross, worked on http://gn2-test3.genenetwork.org/
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py8
1 files changed, 6 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index e1aa290b..9909b6d4 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -128,7 +128,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(type == '4-way'){
genocodes <- c('1','2','3','4')
} else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
@@ -139,7 +139,11 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
- cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ if(type == '4-way'){
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else{
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ }
if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
return(cross)
}