Merge and filter motifbreakR + echolocatoR results

Source: R/MOTIFBREAKR_filter.R

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.

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)
#> genome_build set to hg19 by default.
#> Using genome_build hg19
#> + MOTIFBREAKR:: Using pre-existing tmp file.
mb_res_filt <- MOTIFBREAKR_filter(mb_res = mb_res,
                                  merged_DT = merged_DT)
#> Creating 'risk_' columns
#> + MOTIFBREAKR 1 SNPs in results.
#> + MOTIFBREAKR 1 SNPs in results @ `snp_filter='Support>0'`
#> + MOTIFBREAKR 0 SNPs in results @ `pvalue_threshold=1e-04`
#> + MOTIFBREAKR 0 SNPs in results @ `qvalue_threshold=0.05`