Improper header in pheno dataframe with single column pheno file about qtl HOT 3 CLOSED

@fdchevalier I've got it fixed; thanks!

from qtl.

Thanks! I really appreciate the excellent example.

The problem is in lines 199-201 of read.cross.csvs.R:

colnames(pheno) <- unlist(pheno[1,])
pheno <- apply(pheno, 2, function(a) { a[!is.na(a) & a==""] <- NA; a })
pheno <- as.data.frame(pheno[-1,], stringsAsFactors=TRUE)

The apply() function with a single-column data frame messes up the column names.

from qtl.

I am glad the example helped.

So, a simple fix could be storing the column names and setting them after the data frame is created. Something like:

pnames <- unlist(pheno[1,])
pheno <- apply(pheno, 2, function(a) { a[!is.na(a) & a==""] <- NA; a })
pheno <- as.data.frame(pheno[-1,], stringsAsFactors=TRUE)
colnames(pheno) <- pnames

Happy to send a PR your way if you would like.

from qtl.