factorFootprints: plot ATAC-seq footprints infer factor occupancy genome wide
In jaime11/Transcription-Factor-Footprinting: ATAC-seq Quality Control

Description Usage Arguments Value Author(s) References Examples

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

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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)

`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.

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.

Jianhong Ou

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.

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)