factorFootprints {ATACseqQC} | R Documentation

## plot ATAC-seq footprints infer factor occupancy genome wide

### Description

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

### Usage

    factorFootprints(
      bamfiles,
      index = bamfiles,
      pfm,
      genome,
      min.score = "95%",
      bindingSites,
      seqlev = paste0("chr", c(1:22, "X", "Y")),
      upstream = 100,
      downstream = 100,
      maxSiteNum = 1e+06,
      anchor = "cut site",
      group = "strand",
      ...
    )

### 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.
`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.
`maxSiteNum` | numeric(1). Maximal number of predicted binding sites. if predicted binding sites is more than this number, top maxSiteNum binding sites will be used.
`anchor` | "cut site" or "fragment center". If "fragment center" is used, the input bamfiles must be paired-end.
`group` | Group information for the bamfiles. Default by strand. Otherwise, a factor or vector of characters with same length of bamfiles. The group is limited to 2 groups.
`...` | xlab, legTitle, xlim or ylim could be used by plotFootprints

### 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, Julie Zhu

### 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")
    library(MotifDb)
    CTCF <- query(MotifDb, c("CTCF"))
    CTCF <- as.list(CTCF)
    library(BSgenome.Hsapiens.UCSC.hg19)
    factorFootprints(bamfile, pfm=CTCF[[1]],
                    genome=Hsapiens,
                    min.score="95%", seqlev="chr1",
                    upstream=100, downstream=100)

[Package ATACseqQC version 1.11.8 Index]