aggregateMatches: aggregateMatches

In ETHZ-INS/scanMiR: scanMiR

aggregateMatches

Description

Aggregates miRNA binding sites with log_kd values to predict transcript repression. See the vignette for more detail.

Usage

aggregateMatches(
  m,
  a = 0.007726,
  b = 0.5735,
  c = 0.181,
  p3 = 0.051,
  coef_utr = 0,
  coef_orf = 0,
  p3.range = c(3L, 8L),
  keepSiteInfo = TRUE,
  toInt = FALSE,
  BP = NULL
)

Arguments

m	A GRanges or data.frame of matches as returned by 'findSeedMatches'.
a	The relative concentration of unbound AGO-miRNA complexes.
b	Factor specifying the additional repression by a single bound AGO.
c	Penalty for sites that are found within the ORF region.
p3	Factor specifying additional repression due to 3p alignment.
coef_utr	Factor specifying additional repression due to UTR length.
coef_orf	Factor specifying additional repression due to ORF length.
p3.range	Range used for 3p alignment.
keepSiteInfo	Logical; whether to return information about site types (default = TRUE). Ignored if 'm' does not contain 'log_kd' values
toInt	Logical; whether to convert repression scores to integers (default = FALSE).
BP	Pass 'BiocParallel::MulticoreParam(ncores, progressbar=TRUE)' to enable multithreading. Note that in addition, 'aggregateMatches' uses the data.table package, which is often set to use multi-threading by default (which would be multiplied by threads determined by 'BP'). See setDTthreads for more information.

Value

a data.frame containing aggregated repression values and/or information about the numbers and types of matches

Examples

# we create mock RNA sequences and seeds:
seqs <- getRandomSeq(n=10)

# load sample KdModel
data(SampleKdModel)

# find matches
matches <- findSeedMatches(seqs, SampleKdModel)

# aggregate matches
aggregateMatches(matches)

ETHZ-INS/scanMiR documentation built on April 16, 2024, noon