factorFootprints {ATACseqQC} | R Documentation |
Aggregate ATAC-seq footprint for a given motif generated over binding sites within the genome.
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", ...)
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. |
... |
xlab, legTitle, xlim or ylim could be used by plotFootprints |
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, Julie Zhu
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.
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)