ssvFetchBigwig.single {seqsetvis} | R Documentation |
ssvFetchBigwig.single
Gets values for each region of the query
GRanges (qgr
). Values correspond to the center of each window of
size win_size
. A tidy formatted data.table
object is returned suitable for plotting using ggplots.
ssvFetchBigwig.single( bw_file, 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, force_skip_centerFix = FALSE )
bw_file |
The character vector path to bigwig files to read from. |
qgr |
Set of GRanges to query. For valid results the width of each
interval should be identical and evenly divisible by |
win_size |
The window size that evenly divides widths in |
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. |
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". |
if qgr
contains the range chr1:1-100 and win_size
is
10, values from positions chr1 5,15,25...85, and 95 will be retrieved
from bw_file
A GRanges (or data.table if specified) containing fetched values.