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]