findGRangesCols {TCGAutils} | R Documentation |
This function attempts to match chromosome, start position, end position and
strand names in the given character vector. Modified helper from the
GenomicRanges
package.
findGRangesCols( df_colnames, seqnames.field = c("seqnames", "seqname", "chromosome", "chrom", "chr", "chromosome_name", "seqid", "om"), start.field = "start", end.field = c("end", "stop"), strand.field = "strand", ignore.strand = FALSE )
df_colnames |
A |
seqnames.field |
A |
start.field |
A |
end.field |
A |
strand.field |
A |
ignore.strand |
logical (default FALSE) whether to ignore the strand field in the data |
Index positions vector indicating columns with appropriate names
myDataColNames <- c("Start_position", "End_position", "strand", "chromosome", "num_probes", "segment_mean") findGRangesCols(myDataColNames)