produce a coverage RLE given a gene symbol, hg19-based

Source: R/readcov.R

produce a coverage RLE given a gene symbol, hg19-based

read_covg_by_symbol(sym, bamf, radius = 0)

Arguments

sym

a gene symbol
bamf

a path to indexed BAM file
radius

numeric(1) defaulting to zero, upstream/downstream extra reach

Note

Uses genes_df_hg19 to find address of gene.

Examples

if (requireNamespace("RNAseqData.HNRNPC.bam.chr14")) {
  f1 = RNAseqData.HNRNPC.bam.chr14::RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
  read_covg_by_symbol("HNRNPC", f1)
}

#> integer-Rle of length 107349540 with 1944 runs
#>   Lengths: 21677346        5        2        1 ...        1       13 85611935
#>   Values :        0        1        2        3 ...        2        1        0