filterSegments: Filter segments by minimal size

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Filter segments by minimal size

Description

filterSegments filters out segments below a specified minimal segment size. This can be useful to get rid of boundary effects from the Hidden Markov approach.

Usage

filterSegments(segments, min.seg.width)

Arguments

segments	A GRanges-class object.
min.seg.width	The minimum segment width in base-pairs.

Value

The input model with adjusted segments.

Author(s)

Aaron Taudt

Examples

## Load an HMM
file <- list.files(system.file("extdata", "primary-lung", "hmms",
                  package="AneuFinderData"), full.names=TRUE)
hmm <- loadFromFiles(file)[[1]]
## Check number of segments before and after filtering
length(hmm$segments)
hmm$segments <- filterSegments(hmm$segments, min.seg.width=2*width(hmm$bins)[1])
length(hmm$segments)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.