produce a TnT::LineTrack with coverage information for a selected gene+radius

linetrack_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
...	passed to LineTrack, so can include color, etc.

Examples

if (requireNamespace("RNAseqData.HNRNPC.bam.chr14")) {
  f1 = RNAseqData.HNRNPC.bam.chr14::RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
  linetrack_covg_by_symbol("HNRNPC", f1, color="gray")
}
#> Loading required namespace: RNAseqData.HNRNPC.bam.chr14
#> A LineTrack 
#> | Label:	gr
#> | Background:	missing, use 'white'
#> | Height:	70
#> | Data:	
#> |       seqnames     start       end     width   strand       color       key
#> |       <factor> <integer> <integer> <integer> <factor> <character> <integer>
#> |  1       chr14  21677346  21677346         1        *        gray         1
#> |  2       chr14  21677351  21677351         1        *        gray         2
#> |  3       chr14  21677353  21677353         1        *        gray         3
#> |  4       chr14  21677354  21677354         1        *        gray         4
#> |  5       chr14  21677372  21677372         1        *        gray         5
#> |  ...       ...       ...       ...       ...      ...         ...       ...
#> |  1939    chr14  21737581  21737581         1        *        gray      1939
#> |  1940    chr14  21737583  21737583         1        *        gray      1940
#> |  1941    chr14  21737591  21737591         1        *        gray      1941
#> |  1942    chr14  21737592  21737592         1        *        gray      1942
#> |  1943    chr14  21737605  21737605         1        *        gray      1943
#> |             val
#> |       <integer>
#> |  1            0
#> |  2            1
#> |  3            2
#> |  4            3
#> |  5            4
#> |  ...        ...
#> |  1939         9
#> |  1940         7
#> |  1941         4
#> |  1942         2
#> |  1943         1