ssvFetchBamPE.single {seqsetvis} | R Documentation |
fetch a windowed version of a paired-end bam file, returns GRanges In contrast to ssvFetchBam, extension of reads to estimated fragment size is not an issue as each read pair represents a fragment of exact size.
ssvFetchBamPE.single( bam_f, qgr, win_size = 50, win_method = c("sample", "summary")[1], summary_FUN = stats::weighted.mean, anchor = c("left", "left_unstranded", "center", "center_unstranded")[3], return_data.table = FALSE, max_dupes = Inf, min_isize = 1, max_isize = Inf, return_unprocessed = FALSE, return_fragSizes = FALSE, force_skip_centerFix = FALSE, ... )
bam_f |
character or BamFile to load |
qgr |
GRanges regions to fetchs |
win_size |
numeric >=1. pileup grabbed every win_size bp for win_method sample. If win_method is summary, this is the number of windows used (confusing, sorry). |
win_method |
character. one of c("sample", "summary"). Determines if
|
summary_FUN |
function. only relevant if win_method is "summary".
passed to |
anchor |
character, one of c("center", "center_unstranded", "left", "left_unstranded") |
return_data.table |
logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE. |
max_dupes |
numeric >= 1. duplicate reads by strandd start position over this number are removed, Default is Inf. |
min_isize |
integer. Read pairs must have an isize greater than or equal to this value. Default is 1. |
max_isize |
integer. Read pairs must have an isize less than or equal to this value. Default is Inf. |
return_unprocessed |
boolean. if TRUE returns read alignment in data.table. Default is FALSE. |
return_fragSizes |
boolean. if TRUE returns fragment sizes for all reads per region. |
force_skip_centerFix |
boolean, if TRUE all query ranges will be used "as is". This is already the case by default if win_method == "summary" but may have applications where win_method == "sample". |
... |
passed to Rsamtools::ScanBamParam() |
tidy GRanges (or data.table if specified) with pileups from bam file. pileup is calculated only every win_size bp.