Run motifbreakR

motifbreakR is a package to predict how much a SNP will disrupt a transcription factor binding motif (if it falls within one). Notes:

BSgenome

Users must manually run library(BSgenome) before running any motifbreakR functions to successfully use this tool.

threshold=

If filterp=TRUE, this argument indicates the p-value threshold. If filterp=FALSE, this argument instead indicates the pct threshold.

MOTIFBREAKR(
  rsid_list,
  results_dir = file.path(tempdir(), "results"),
  pwmList = NULL,
  pwmList_max = NULL,
  genome_build = NULL,
  organism = "Hsapiens",
  threshold = 0.85,
  show.neutral = FALSE,
  method = "default",
  calculate_pvals = TRUE,
  force_new = FALSE,
  background = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  granularity = NULL,
  nThread = 1,
  verbose = TRUE
)

Source

Publication GitHub Vingette

Arguments

rsid_list

RSIDs of SNPs to test for motif disruption between the reference and alternative alleles..

results_dir

Directory where results should be saved as a file named: <results_dir>/_genome_wide/motifbreakR/motifbreakR_results.rds. If NULL, results will not be saved to disk.

pwmList

An object of class TFBSTools::MotifList containing position weight matrices. If NULL, defaults to MotifDb::MotifDb.

pwmList_max

Limit the maximum number of PWM datasets tested (e.g. 10). If NULL, no limit it set.

genome_build

Genome build to use.

organism

Only include datasets in the pwmList performed in a particular organism.

threshold

A numeric value used as a threshold for filtering results.

show.neutral

Logical. Include neutral effects in results.

method

Character string specifying the method for scoring effects.

calculate_pvals

Calculate p-values for all SNPs tested. WARNING: May take a long time if many SNPs and/or PWM are selected.

force_new

If results of the same name already exist, overwrite them with new analyses (TRUE). Otherwise, import the existing results and skip the analyses (default: FALSE).

background

A named numeric vector of background nucleotide frequencies (A, C, G, T) summing to 1.

granularity

Granularity for p-value calculation. If NULL, a default is chosen automatically.

nThread

Number of threads to parallelize analyses across.

verbose

Print messages.

Value

Motif disruption predictions in GRanges format.

See also

Other motifbreakR: MOTIFBREAKR_filter_by_metadata(), MOTIFBREAKR_summarize()

Examples

if (FALSE) { # \dontrun{
library(BSgenome) ## <-- IMPORTANT!
#### Example fine-mapping results ####
merged_DT <- echodata::get_Nalls2019_merged()
#### Run motif analyses ####
mb_res <- MOTIFBREAKR(rsid_list = c("rs11175620"),
                      # limit the number of datasets tested
                      # for demonstration purposes only
                      pwmList_max = 4,
                      calculate_pvals = FALSE)
} # }