README.md

In PriceLab/GeneRegulationUtilities: snpFoot

snpFoot

An R package with miscellaneous functions and public data for the exploration and analysis of gene regulation

findTFsInFootprints: for selected transcription factors, find DNase I footprints in which they may bind

library(GeneRegulationUtilities)
data(tbl.fpAnnotated)  # may take 30 seconds or so: > 4M DNAse I footprints with TF motifs
data(tbl.motifToMultipleGenes)  # much quicker: maps motif identifiers to gene symbols (from Seth)

target.tfs <- c("POU5F2", "SATB2", "HLF", "SOX4", "CUX2")
tbl.out <- findTFsInFootprints(tbl.fpAnnotated, tbl.motifToMultipleGenes, "chr5", 88640561, 89001975, target.tfs)
dim(tbl.out)   # 212 18
head(tbl.out)[, c(1:4, 18)]
        chr      start      end score tfsMatched
3610411 chr5 88643612 88643621  53.5       SOX4
3610412 chr5 88643613 88643621  50.5       SOX4
3610451 chr5 88653378 88653392  52.6       SOX4
3610452 chr5 88653378 88653392  61.2       SOX4
3610456 chr5 88653569 88653578  52.7     POU5F2
3610497 chr5 88656492 88656507  51.1     POU5F2

findSNPsInFootprints: find the footprints which overlap with the specified SNPS

chrom <- "chr19"
min.loc <- 1004844
max.loc <- 1100074
candidate.snps <- c(1007158, 1095102, 1095122, 1095630)
findSNPsInFootprints(tbl.fpAnnotated, tbl.motifToMultipleGenes,
                     chrom, min.loc, max.loc,
                     chrom, candidate.snps,
                     transcriptionFactors=NA,
                     padding=0)

  chr mfpStart  mfpEnd motifStart motifEnd        sequence     name     snp tfsMatched
chr19  1095102 1095131    1095117  1095131 GAGGCCCAGAGGTCG MA0728.1 1095122 NR2F6
chr19  1095630 1095657    1095630  1095643  ACTTCGCCCCCGCC MA0162.2 1095630 EGR1;EGR2;...

Add padding to the search so that snps near footprints are also retured:

findSNPsInFootprints(tbl.fpAnnotated, tbl.motifToMultipleGenes, chrom, min.loc, max.loc, chrom, candidate.snps, transcriptionFactors=NA, padding=10)

  chr mfpStart  mfpEnd motifStart motifEnd        sequence     name     snp tfsMatched
chr19  1095062 1095094    1095062  1095076 CCCCCTCCCTTCCCC MA0516.1 1095102 EGR1;EGR2;...
chr19  1095102 1095131    1095117  1095131 GAGGCCCAGAGGTCG MA0728.1 1095122 NR2F6
chr19  1095630 1095657    1095630  1095643  ACTTCGCCCCCGCC MA0162.2 1095630 EGR1;EGR2;...

Create an igv track from data/tbl.gwasADsnpsInFp.05pval.igap2013.RData

data(tbl.gwasADsnpsInFp.05pval.igap2013)
igv <- igvR()
connected(igv)
displayBedTable(igv, tbl.gwasADsnpsInFp[, c("chr", "snp", "snp")], "gwasFPsnps")

PriceLab/GeneRegulationUtilities documentation built on May 8, 2019, 3:11 p.m.