MOTIFBREAKR_filter: Merge and filter 'motifbreakR' + 'echolocatoR' results

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Merge and filter motifbreakR + echolocatoR results

Description

For each SNP we have at least one allele achieving a p-value<1e-4 threshold that we required. The seqMatch column shows what the reference genome sequence is at that location, with the variant position appearing in an uppercase letter. pctRef and pctAlt display the the score for the motif in the sequence as a percentage of the best score that motif could achieve on an ideal sequence. In other words, (scoreVariant−minscorePWM)/(maxscorePWM−minscorePWM). We can also see the absolute scores for our method in scoreRef and scoreAlt and their respective p-values.

Usage

MOTIFBREAKR_filter(
  mb_res,
  merged_DT,
  filter_by_locus = NULL,
  remove_NA_geneSymbol = TRUE,
  pct_threshold = NULL,
  pvalue_threshold = 1e-04,
  qvalue_threshold = 0.05,
  effect_strengths = NULL,
  snp_filter = "Support>0",
  top_geneSymbol_hits = NULL,
  no_no_loci = NULL,
  verbose = TRUE
)

Arguments

mb_res	Results generated by MOTIFBREAKR, in GRanges format.
merged_DT	Table with columns Locus and SNP to filter mb_res by.
filter_by_locus	Filter mb_res to only include SNPs present in a given Locus (e.g. "BST1"). Set to NULL (default) for not perform any filtering. Requires merged_DT argument to be supplied.
remove_NA_geneSymbol	Remove results where geneSymbol==NA.
pct_threshold	Remove rows below the percentage of the optimal binding score (PCT) threshold.
pvalue_threshold	Remove rows below the raw significance value (p-value) threshold.
qvalue_threshold	Remove rows below the multiple testing-corrected significance value (q-value) threshold.
effect_strengths	Only include results with certain effect strengths.
snp_filter	Condition to filter SNPs by, after mb_res and merged_DT have been merged together into one table.
top_geneSymbol_hits	Only include N top results per gene symbol based on absolute risk_score, where N=top_geneSymbol_hits. If top_geneSymbol_hits=NULL, no such filtering is performed.
no_no_loci	Filter out SNPs contained within specific loci in the merged_DT table.
verbose	Print messages.

Value

data.table with the filtered motif disruption results after merging with merged_DT.

Examples

merged_DT <- echodata::get_Nalls2019_merged()
mb_res <- MOTIFBREAKR(rsid_list = c("rs11175620"),
                      # limit the number of datasets tests 
                      # for demonstration purposes only
                      pwmList_max = 4,
                      calculate_pvals = FALSE)
mb_res_filt <- MOTIFBREAKR_filter(mb_res = mb_res,
                                  merged_DT = merged_DT)

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.