footprintsScanner {ATACseqQC} | R Documentation |
Aggregate ATAC-seq footprint for a bunch of motifs generated over binding sites within the genome.
footprintsScanner(bamfiles, index = bamfiles, bindingSitesList, seqlev = "chr1", upstream = 100, downstream = 100)
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. |
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.
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)