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| author | Danny Arends | 2020-04-29 04:38:42 -0500 |
|---|---|---|
| committer | Danny Arends | 2020-04-29 04:38:42 -0500 |
| commit | 10b8dc7af35f0d221daf121d0e3c0a52d9223368 (patch) | |
| tree | dc29a22d162cd827ea689dfbed0870b282ff97ac | |
| parent | 86d885f5f2e1069a5b1606296a71992805486aec (diff) | |
| download | genenetwork2-10b8dc7af35f0d221daf121d0e3c0a52d9223368.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.py | 8 |
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) } |