enrichedMirTxPairs: enrichedMirTxPairs

In ETHZ-INS/scanMiRApp: scanMiR shiny application

enrichedMirTxPairs

Description

Identifies pairs of miRNA and target transcripts that have an unexpectedly high number of sites.

Usage

enrichedMirTxPairs(m, minSites = 5, max.binom.p = 0.001)

Arguments

m	A GRanges of matches, as produced by findSeedMatches. This will be filtered down to only 8mer and 7mer sites.
minSites	The minimum number of sites for a given miRNA-target pair to be considered.
max.binom.p	The maximum binomial p-value of miRNA-target pairs.

Value

A data.frame of top combinations, including number of sites and the log-transformed binomial p-value.

Examples

# we create a dummy scan (see `runFullScan`)
library(scanMiR)
seqs <- getRandomSeq(n=10)
mirs <- c("TTGTATAA","AGCATTAA")
m <- findSeedMatches(seqs,mirs,verbose=FALSE)
# we look for enriched pairs
res <- enrichedMirTxPairs(m, minSites=1, max.binom.p=1)
res

ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 p.m.