featureAlignedExtendSignal {ChIPpeakAnno} | R Documentation |
extract signals in the given feature ranges from bam files (DNAseq only). The reads will be extended to estimated fragement length.
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
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) } }