quantifyMotifDisruption: Estimate how much PWM binding score is altered by the SNP

In kauralasoo/seqUtils:

Description

Estimate how much PWM binding score is altered by the SNP

Usage

quantifyMotifDisruption(pwm, peak_id, snp_id, peak_metadata,
  peak_sequences, snp_metadata, window_size = 25)

Arguments

pwm	Position weight matrix in TFBSTools format
peak_id	ID of the ATAC peak
snp_id	ID of the variant
peak_metadata	Peak metadata (required columns: gene_id, start)
peak_sequences	DNAStringSet object containing the peak sequences.
snp_metadata	SNP metadata (required columns: snp_id, chr, pos, ref, alt)
window_size	Window size around the SNP

Value

Data frame of binding socres for the reference and alternate versions of the sequence.

kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.