fragLen_calcStranded {seqsetvis} | R Documentation |
calculate fragLen from a bam file for specified regions
fragLen_calcStranded(bam_f, qgr, ma_distance = 21, n_regions = 100, force_no_which = FALSE, include_plot_in_output = FALSE, max_fragLen = 300, ...)
bam_f |
character or BamFile. bam file to read from. .bai index file must be in same directory |
qgr |
GRanges. used as which for ScanBamParam. Can be NULL if it's REALLY important to load the entire bam, force_no_which = TRUE also required. |
ma_distance |
numeric (integer) range to use for movingRange. Default is 21. |
n_regions |
numeric (integer) it's generally overkill to pull all regions at this stage and will slow calculation down. Default is 100. |
force_no_which |
logical. if TRUE and qgr is also NULL, the entire bam will be read. |
include_plot_in_output |
if TRUE ouptut is a list of fragLen and a ggplot showing values considered by calculation. Default is FALSE. |
max_fragLen |
numeric. The maximum fragLen to calculate for. Calculation time is directly proportional to this number. Default is 300. |
... |
passed to Rsamtools::ScanBamParam, can't be which or what. |
numeric fragment length
bam_file = system.file("extdata/test.bam", package = "seqsetvis") qgr = CTCF_in_10a_overlaps_gr[1:5] fragLen_calcStranded(bam_file, qgr) #if plot is included, a list is returned, item 2 is the plot fragLen_calcStranded(bam_file, qgr, include_plot_in_output = TRUE)[[2]]