Description Usage Arguments Value Author(s) See Also Examples
View source: R/featureAlignedExtendSignal.R
extract signals in the given feature ranges from bam files (DNAseq only). The reads will be extended to estimated fragement length.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | featureAlignedExtendSignal(
bamfiles,
index = bamfiles,
feature.gr,
upstream,
downstream,
n.tile = 100,
fragmentLength,
librarySize,
pe = c("auto", "PE", "SE"),
adjustFragmentLength,
gal,
...
)
|
bamfiles |
The file names of the 'BAM' ('SAM' for asBam) files to be processed. |
index |
The names of the index file of the 'BAM' file being processed; this is given without the '.bai' extension. |
feature.gr |
An object of GRanges with identical width. |
upstream, downstream |
upstream or dwonstream from the feature.gr. |
n.tile |
The number of tiles to generate for each element of feature.gr, default is 100 |
fragmentLength |
Estimated fragment length. |
librarySize |
Estimated library size. |
pe |
Pair-end or not. Default auto. |
adjustFragmentLength |
A numberic vector with length 1. Adjust the fragments/reads length to. |
gal |
A GAlignmentsList object or a list of GAlignmentPairs. If bamfiles is missing, gal is required. |
... |
Not used. |
A list of matrix. In each matrix, each row record the signals for corresponding feature.
Jianhong Ou
See Also as featureAlignedSignal
,
estLibSize
, estFragmentLength
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | if(interactive() || Sys.getenv("USER")=="jianhongou"){
path <- system.file("extdata", package="MMDiffBamSubset")
if(file.exists(path)){
WT.AB2 <- file.path(path, "reads", "WT_2.bam")
Null.AB2 <- file.path(path, "reads", "Null_2.bam")
Resc.AB2 <- file.path(path, "reads", "Resc_2.bam")
peaks <- file.path(path, "peaks", "WT_2_Macs_peaks.xls")
estLibSize(c(WT.AB2, Null.AB2, Resc.AB2))
feature.gr <- toGRanges(peaks, format="MACS")
feature.gr <- feature.gr[seqnames(feature.gr)=="chr1" &
start(feature.gr)>3000000 &
end(feature.gr)<75000000]
sig <- featureAlignedExtendSignal(c(WT.AB2, Null.AB2, Resc.AB2),
feature.gr=reCenterPeaks(feature.gr, width=1),
upstream = 505,
downstream = 505,
n.tile=101,
fragmentLength=250,
librarySize=1e9)
featureAlignedHeatmap(sig, reCenterPeaks(feature.gr, width=1010),
zeroAt=.5, n.tile=101)
}
}
|
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