findTFBS: Find putative transcription factor binding sites

In andigoni/MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Description

Detects JASPAR's transcription factor binding sites (core collection), co-localized with input data. Both sequence strands are examined. The analysis can be restricted to promoters (use 'uptss' and 'down.tss' to define promoter length, relative to transcription start site) and CpG islands of the human genome (hg19).

Usage

findTFBS(bed.data, persim = 0.8, offset = 12, target = "PROMOTER",
  up.tss = 1000, down.tss = 100, mcores = NULL, tf.ID = NULL)

Arguments

bed.data	A data frame containing input bed-formatted data
persim	Minimum similarity with transcription factors consensus matrices (default:0.8, range in [0,1])
offset	Number of nucleotides expanded in each direction (default:12, min:5, max:100)
target	Search for transcription factor binding sites on specific regions. 'PROMOTER': selects sites located in promoter regions, 'CGI': selects sites in CpG islands, 'ALL': No filtering is applied (time-consuming for large datasets) (default: "PROMOTER")
up.tss	Number of nucleotides upstream transcription start site (Only when target="PROMOTER" is set, default: 1000)
down.tss	Number of nucleotides downstream transcription start site (Only when target="PROMOTER" is set, default: 100)
mcores	Number of cores to be used (default: maximum available)
tf.ID	A vector of JASPAR transcription factors identifiers to search for (default: all)

Value

1/ Data frame containing the transcription factors identified in each sequence, their position and binding score (input to 'plotTF' function)

2/ Data frame of the detected transcription factor binding sites per sequence (input to 'meinter' function)

andigoni/MeinteR documentation built on Oct. 1, 2021, 9:33 p.m.