summarizePatternInPeaks: Output a summary of the occurrence of each pattern in the...

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Output a summary of the occurrence of each pattern in the sequences.

Usage

summarizePatternInPeaks(
  patternFilePath,
  format = "fasta",
  skip = 0L,
  BSgenomeName,
  peaks,
  outfile,
  append = FALSE
)

Arguments

patternFilePath	A character vector containing the path to the file to read the patterns from.
format	Either "fasta" (the default) or "fastq"
skip	Single non-negative integer. The number of records of the pattern file to skip before beginning to read in records.
BSgenomeName	BSgenome object. Please refer to available.genomes in BSgenome package for details
peaks	GRanges containing the peaks
outfile	A character vector containing the path to the file to write the summary output.
append	TRUE or FALSE, default FALSE

Value

A data frame with 3 columns as n.peaksWithPattern (number of peaks with the pattern), n.totalPeaks (total number of peaks in the input) and Pattern (the corresponding pattern). The summary will consider both strand (including reverse complement).

Author(s)

Lihua Julie Zhu

Examples

    peaks = GRanges(seqnames=c("NC_008253", "NC_010468"), 
                    IRanges(start=c(100, 500), end=c(300, 600), 
                               names=c("peak1", "peak2")))
    filepath =system.file("extdata", "examplePattern.fa", 
                          package="ChIPpeakAnno")
    library(BSgenome.Ecoli.NCBI.20080805)
    summarizePatternInPeaks(patternFilePath=filepath, format="fasta", 
                            skip=0L, BSgenomeName=Ecoli, peaks=peaks)

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.