getTagMatrix | R Documentation |
calculate the tag matrix
getTagMatrix(
peak,
upstream,
downstream,
windows,
type,
by,
TxDb = NULL,
weightCol = NULL,
nbin = NULL,
verbose = TRUE,
ignore_strand = FALSE
)
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', or specified by users |
TxDb |
TxDb or self-made granges object, served as txdb |
weightCol |
column name of weight, default is NULL |
nbin |
the amount of nbines |
verbose |
print message or not |
ignore_strand |
ignore the strand information or not |
getTagMatrix()
function can produce the matrix for visualization.
peak
stands for the peak file.
window
stands for a collection of regions that users want to look into.
Users can use window
to capture the peak of interest.
There are two ways to input window
.
The first way is that users can use
getPromoters()/getBioRegion()/makeBioRegionFromGranges()
to
get window
and put it into getTagMatrix()
.
The second way is that users can use getTagMatrix()
to
call getPromoters()/getBioRegion()/makeBioRegionFromGranges()
. In this way
users do not need to input window
parameter but they need to input
txdb
.
txdb
is a set of packages contained annotation
of regions of different genomes. Users can
get the regions of interest through specific functions. These specific functions
are built in getPromoters()/getBioRegion()
. Many regions can not be gain
through txdb
, like insulator and enhancer regions.
Users can provide these regions in the form of granges object.
These self-made granges object will be passed to TxDb
parameter and they will
be passed to makeBioRegionFromGranges()
to produce the window
.
In a word, TxDb
parameter is a reference information. Users can
pass txdb object
or self-made granges into it.
Details see getPromoters
,getBioRegion
and makeBioRegionFromGranges
upstream
and downstream
parameter have different usages:
(1) window
parameter is provided,
if type == 'body'
, upstream
and downstream
can use to extend
the flank of body region.
if type == 'start_site'/'end_site'
, upstream
and downstream
do not
play a role in getTagMatrix()
function.
(2) window
parameter is missing,
if type == 'body'
, upstream
and downstream
can use to extend
the flank of body region.
if type == 'start_site'/'end_site'
, upstream
and downstream
refer to
the upstream and downstream of the start_site or the end_site.
weightCol
refers to column in peak file. This column acts as a weight vaule. Details
see https://github.com/YuLab-SMU/ChIPseeker/issues/15
nbin
refers to the number of bins. getTagMatrix()
provide a binning method
to get the tag matrix.
tagMatrix
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