getTagMatrix {ChIPseeker} | R Documentation |
calculate the tag matrix
getTagMatrix( peak, upstream, downstream, windows, type, by, TxDb = NULL, weightCol = NULL, nbin = NULL, verbose = TRUE, flip_minor_strand = TRUE )
peak |
peak peak file or GRanges object |
upstream |
the distance of upstream extension |
downstream |
the distance of downstream extension |
windows |
a collection of region |
type |
one of "start_site", "end_site", "body" |
by |
one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' |
TxDb |
TxDb |
weightCol |
column name of weight, default is NULL |
nbin |
the amount of nbines |
verbose |
print message or not |
flip_minor_strand |
whether flip the orientation of minor strand |
tagMatrix