viewTargetAlignment {scanMiR} | R Documentation |
viewTargetAlignment
viewTargetAlignment( m, miRNA, seqs = NULL, flagBulgeMatches = FALSE, maxBulgeSize = 9L, maxBulgeDiff = 4L, min3pMatch = 3L, hideSingletons = FALSE, UGsub = TRUE, ..., outputType = c("print", "data.frame", "plot", "ggplot") )
m |
A GRanges of length 1 giving the information for a given match, as
produced by |
miRNA |
A miRNA sequence, or a |
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'. |
Returns nothing 'outputType="print"'. If 'outputType="data.frame"', returns a data.frame containing the alignment strings; if 'outputType="plot"' returns a 'ggplot' object.
data(SampleKdModel) seq <- c(seq1="CGACCCCTATCACGTCCGCAGCATTAAAT") m <- findSeedMatches(seq, SampleKdModel, verbose=FALSE) viewTargetAlignment(m, miRNA=SampleKdModel, seqs=seq)