viewTargetAlignment {scanMiR}R Documentation

viewTargetAlignment

Description

viewTargetAlignment

Usage

viewTargetAlignment(
  m,
  miRNA,
  seqs = NULL,
  flagBulgeMatches = FALSE,
  maxBulgeSize = 9L,
  maxBulgeDiff = 4L,
  min3pMatch = 3L,
  hideSingletons = FALSE,
  UGsub = TRUE,
  ...,
  outputType = c("print", "data.frame", "plot", "ggplot")
)

Arguments

m

A GRanges of length 1 giving the information for a given match, as produced by findSeedMatches.

miRNA

A miRNA sequence, or a KdModel object of the miRNA corresponding to the match in 'm'; alternatively, a KdModelList including the model.

seqs

The sequences corresponding to the seqnames of 'm'. Not needed if 'm' contains the target sequences.

flagBulgeMatches

Logical; whether to flag matches inside the bulge (default FALSE)

maxBulgeSize

The maximum bulge size to consider (default none)

maxBulgeDiff

The maximum difference between miRNA and target bulges

min3pMatch

The minimum 3' alignment for any to be plotted

hideSingletons

Logical; whether to hide isolated single base-pair matches

UGsub

Logical; whether to show U-G matches

...

Passed to 'text' if 'outputType="plot"'.

outputType

Either 'print' (default, prints to console), 'data.frame', or 'plot'.

Value

Returns nothing 'outputType="print"'. If 'outputType="data.frame"', returns a data.frame containing the alignment strings; if 'outputType="plot"' returns a 'ggplot' object.

Examples

data(SampleKdModel)
seq <- c(seq1="CGACCCCTATCACGTCCGCAGCATTAAAT")
m <- findSeedMatches(seq, SampleKdModel, verbose=FALSE)
viewTargetAlignment(m, miRNA=SampleKdModel, seqs=seq)

[Package scanMiR version 0.99.26 Index]