peakIdenSeq: Peak Identifier Plus

In DanielRivasMD/CopperGenomicFunctions: Compilation of R functions for Genomic Data

Description

Identifies peaks in a vector of number above a defined threshold 'dThreshold'. Additionally, calculates 'min', 'mean', 'sum' and coordinates in indixes (ix) and nucleotides (nt) given 'dBinSize' and 'dBinOverlaps' assuming it is dealing with overlaping windows.

Usage

peakIdenSeq(fSeq, dThreshold = NULL, dBinSize = NULL, dBinOverlaps = NULL)

Arguments

fSeq	Numeric vector
dThreshold	Threshold for peak identification. Default = 1
dBinSize	Defines bin size assuming fSeq is a vector of sliding windows. Default = 500
dBinOverlaps	Defines bin overlaps assuming fSeq is a vector of sliding windows. Default = 10

Value

data.frame with following columns:

1. peakNo

2. seqMax

3. seqMin

4. seqMean

5. seqSum

6. lowerLimIx

7. upperLimIx

8. peakLengthIx

9. peakLengthNt

See Also

peakIden

Examples

x <- sample(0:5, 100, replace = TRUE, prob = c(5, rep(1, 5)))
peakIdenSeq(
x,
dThreshold = 1,
dBinSize = 10,
dBinOverlaps = 1
)

DanielRivasMD/CopperGenomicFunctions documentation built on Nov. 19, 2021, 10:11 p.m.