mm10 rmsk colname failure

[AMChalkie]

R.3.5.2.>features.rmsk <- getFeatures(tables=c("rmsk"),genome="mm10", cachedir=cachedir,sync=TRUE)
|==================================================|
Error in setnames(x, c("chrom", "chromStart", "chromEnd"), c("chr", "start", :
Items of 'old' not found in column names: chrom,chromStart,chromEnd
R.3.5.2.>
R.3.5.2.>traceback()
6: stop("Items of 'old' not found in column names: ", paste(old[is.na(i)],
collapse = ","))
5: setnames(x, c("chrom", "chromStart", "chromEnd"), c("chr", "start",
"end"))
4: FUN(X[[i]], ...)
3: lapply(tab.dt, togr)
2: lapply(tab.dt, togr)
1: getFeatures(tables = c("rmsk"), genome = genome, cachedir = cachedir,
sync = TRUE)

Suggested partial fix:

if ("chrom" in colnames(x)){
setnames(x, c("chrom"), c("chr"))
} else {
stopifnot("chr" in colnames(x))
}
setnames(x, c("chromStart", "chromEnd"), c("start", "end"))

[jeffbhasin]

Hello,

I believe the rmsk table has a different schema, and causes this error. When I have needed rmsk I have used the underlying goldmine:::getUCSCTable() function. This can pull the table data, but will not adjust for 0-based start coordinates the way getFeatures() does. However, this way the rmsk data can still be pulled from within R and the column names could be changed manually. This is just a workaround, the code you have could also provide a fix. Please make a pull request if you think you could get getFeatures() working for the "rmsk" table in this manner.

Jeff