diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 7 |
1 files changed, 6 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 9909b6d4..c1a56787 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -140,11 +140,16 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file require(qtl) if(type == '4-way'){ + cat('Loading in as 4-WAY\n') cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross }else{ + cat('Loading in as normal\n') 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 + if(type == 'riset'){ + cat('Converting to RISELF\n') + cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl + } return(cross) } """ % (dataset.group.genofile)) |