diff options
Diffstat (limited to 'scripts/rqtl_wrapper.R')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 13 |
1 files changed, 9 insertions, 4 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index b7a9ae0..13c2684 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -202,14 +202,19 @@ if (!is.null(opt$addcovar)) { name <- paste0("T_", covarDescr[x, 1]) # The covar description file doesn't have T_ in trait names (the cross object does) type <- covarDescr[x, 2] if(type == "categorical"){ - if(length(table(covars[,name])) > 2){ # More then 2 levels create the model matrix for the factor - mdata <- data.frame(toExpand = as.factor(covars[, name])) + verbose_print('Binding covars to covars\n') + if (nrow(covarDescr) < 2){ + this_covar = covars + } else { + this_covar = covars[,name] + } + if(length(table(this_covar)) > 2){ # More then 2 levels create the model matrix for the factor + mdata <- data.frame(toExpand = as.factor(this_covar)) options(na.action='na.pass') modelmatrix <- model.matrix(~ toExpand + 0, mdata)[,-1] covars <- cbind(covars, modelmatrix) }else{ # 2 levels? just bind the trait as covar - verbose_print('Binding covars to covars\n') - covars <- cbind(covars, covars[,name]) + covars <- cbind(covars, this_covar) } } } |