findGRangesCols: Obtain minimum necessary names for the creation of a...
In TCGAutils: TCGA utility functions for data management

Description Usage Arguments Value Examples

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 `character` vector of names in a dataset
`seqnames.field`	A `character` vector of the chromosome name
`start.field`	A `character` vector that indicates the column name of the start positions of ranged data
`end.field`	A `character` vector that indicates the end position of ranged data
`strand.field`	A `character` vector of the column name that indicates the strand type
`ignore.strand`	logical (default FALSE) whether to ignore the strand field in the data

Index positions vector indicating columns with appropriate names

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myDataColNames <- c("Start_position", "End_position", "strand",
                 "chromosome", "num_probes", "segment_mean")
findGRangesCols(myDataColNames)