shiftTx: Shift over transcripts

In yue-wang-biomath/RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Shift over transcripts

Description

Calculate positional shifting over transcript regions.

Usage

shiftTx(regions, start, width, direction, strand)

Arguments

regions	A feature set following the format indicated in vignette section 3. Either to be GRanges or GRangesList.
start	Starting positions. Each value represents a starting position in each input feature.
width	Widths. Each value represents a width of each region to be picked from each feature.
direction	Either to be character "left" or "right", which means the direction to which the starting position is shifting. The former means moving to the direction of 5' while the latter means moving to 3'.
strand	The strand type of the transcripts. It receives "+" or "-".

Value

A Granges object.

Examples

# Take five transcripts.
# Extract the last 200 nt regions from their CDS part.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
trans.id.pstv <- c("170", "782", "974", "1364", "1387")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

# download the CDS part of all transcriptome
cds.tx0 <- cdsBy(txdb, use.names = FALSE)

# pick the CDS part of these five transcripts
cds.p <- cds.tx0[trans.id.pstv]

width <- 200
start <- as.numeric(max(end(cds.p)))
R.cds.last200 <- shiftTx(cds.p, start = start, width = width, direction = 'left', strand = "+")

yue-wang-biomath/RgnTX documentation built on Aug. 24, 2023, 1:12 p.m.