factorFootprints: plot ATAC-seq footprints infer factor occupancy genome wide

Description Usage Arguments Value Author(s) References Examples

View source: R/factorFootprints.R

Description

Aggregate ATAC-seq footprint for a given motif generated over binding sites within the genome.

Usage

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factorFootprints(bamfiles, index = bamfiles, pfm, genome,
  min.score = "95%", bindingSites, seqlev = paste0("chr", c(1:22, "X",
  "Y")), upstream = 100, downstream = 100)

Arguments

bamfiles

A vector of characters indicates the file names of bams.

index

The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.

pfm

A Position frequency Matrix represented as a numeric matrix with row names A, C, G and T.

genome

An object of BSgenome.

min.score

The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "95 score or as a single number. See matchPWM.

bindingSites

A object of GRanges indicates candidate binding sites (eg. the output of fimo).

seqlev

A vector of characters indicates the sequence levels.

upstream, downstream

numeric(1) or integer(1). Upstream and downstream of the binding region for aggregate ATAC-seq footprint.

Value

an invisible list of matrixes with the signals for plot. It includes: - signal mean values of coverage for positive strand and negative strand in feature regions - spearman.correlation spearman correlations of cleavage counts in the highest 10-nucleotide-window and binding prediction score. - bindingSites predicted binding sites.

Author(s)

Jianhong Ou

References

Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., Dent, S., He, X. and Li, W., 2013. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome research, 23(2), pp.341-351.

Examples

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shiftedBamfile <- system.file("extdata", "GL1.bam",
                             package="ATACseqQC")
library(MotifDb)
CTCF <- query(MotifDb, c("CTCF"))
CTCF <- as.list(CTCF)
library(BSgenome.Hsapiens.UCSC.hg19)
factorFootprints(shiftedBamfile, pfm=CTCF[[1]],
                genome=Hsapiens,
                min.score="95%", seqlev="chr1",
                upstream=100, downstream=100)

Bioconductor-mirror/ATACseqQC documentation built on July 28, 2017, 3:23 a.m.