footprintsScanner {ATACseqQC}R Documentation

scan ATAC-seq footprints infer factor occupancy genome wide

Description

Aggregate ATAC-seq footprint for a bunch of motifs generated over binding sites within the genome.

Usage

footprintsScanner(bamfiles, index = bamfiles, bindingSitesList,
  seqlev = "chr1", upstream = 100, downstream = 100)

Arguments

bamfiles

A vector of characters indicates the file names of bams. All the bamfiles will be pulled together.

index

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

bindingSitesList

A object of GRangesList 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


bamfile <- system.file("extdata", "GL1.bam",
                       package="ATACseqQC")
bsl <- system.file("extdata", "jolma2013.motifs.bindingList.95.rds",
                  package="ATACseqQC")
bindingSitesList <- readRDS(bsl)
footprintsScanner(bamfile, bindingSitesList=bindingSitesList)


[Package ATACseqQC version 1.6.4 Index]