Package 'txcutr'

Title: Transcriptome CUTteR
Description: Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.
Authors: Mervin Fansler [aut, cre]
Maintainer: Mervin Fansler <[email protected]>
License: GPL-3
Version: 1.13.0
Built: 2024-12-19 04:40:24 UTC
Source: https://github.com/bioc/txcutr

Help Index

Clip Transcript to Given Length

Description

Internal function for operating on individual GRanges, where ranges represent exons in a transcript. This is designed to be used in an *apply function over a GRangesList object.

Usage

.clipTranscript(gr, maxTxLength)

Arguments

gr

a GRanges object
maxTxLength

a positive integer

Value

the clipped GRanges object

Convert GRanges to Single Range

Description

Convert GRanges to Single Range

Usage

.fillReduce(gr, validate = TRUE)

Arguments

gr

a GRanges with ranges to be merged.
validate

logical determining whether entries should be checked for compatible seqnames and strands.

Details

The validation assumes seqnames and strand are Rle objects.

Value

GRanges with single interval

Efficient Metadata Columns Mutation

Description

Efficient Metadata Columns Mutation

Usage

## S4 method for signature 'CompressedGRangesList'
.mutateEach(grl, ...)

Arguments

grl

a CompressedGRangesList
...

named list of vectors to insert as metadata columns on each element GRanges. Each vector length must match the length of the GRangesList.

Value

a CompressedGRangesList with all element GRanges updated with supplied metadata columns

Propagate Transcript Merge Map

Description

Propagate Transcript Merge Map

Usage

.propagateMap(df, MAXITERS = 1000)

Arguments

df

a data.frame with columns tx_in and tx_out
MAXITERS

a numeric controlling the maximum number of iterations

Value

a converged data.frame, such that, tx_out is not present in any tx_in

Export Transcriptome as FASTA

Description

Export Transcriptome as FASTA

Usage

exportFASTA(txdb, genome, file, ...)

Arguments

txdb

a TxDb object representing a transcriptome annotation
genome

a BSgenome object from which to extract sequences
file

a string for output FASTA file. File names ending in ".gz" will automatically use gzip compression.
...

additional arguments to pass through to writeXStringSet

Value

The txdb argument is invisibly returned.

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
library(BSgenome.Scerevisiae.UCSC.sacCer3)

## load annotation and genome
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
sacCer3 <- BSgenome.Scerevisiae.UCSC.sacCer3

## restrict to 'chrI' transcripts (makes for briefer example runtime)
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)

## export uncompressed
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".fa")
exportFASTA(txdb_w500, sacCer3, outfile)

## export compressed
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".fa.gz")
exportFASTA(txdb_w500, sacCer3, outfile)

Export GTF

Description

Exports a TxDb annotation to a GTF file

Usage

exportGTF(txdb, file, source = "txcutr")

Arguments

txdb

transcriptome to be output
file

a string or connection to output GTF file. Automatically recognizes strings ending with ".gz" for zipped output.
source

a string to go in the source column

Value

The txdb argument is invisibly returned.

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

## restrict to 'chrI' transcripts
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)

## export uncompressed
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".gtf")
exportGTF(txdb_w500, outfile)

## export compressed
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".gtf.gz")
exportGTF(txdb_w500, outfile)

Export Merge Table for Transcriptome

Description

Export Merge Table for Transcriptome

Usage

exportMergeTable(txdb, file, minDistance = 200L)

Arguments

txdb

a TxDb object representing a transcriptome annotation
file

a string or connection to output TSV file. Automatically recognizes strings ending with ".gz" for zipped output.
minDistance

the minimum separation to regard overlapping transcripts as unique.

Value

The txdb argument is invisibly returned.

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

## restrict to 'chrI' transcripts (makes for briefer example runtime)
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)

## export plain format
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".tsv")
exportMergeTable(txdb_w500, outfile)

## export compressed format
outfile <- tempfile("sacCer3.sgdGene.w500", fileext=".tsv.gz")
exportMergeTable(txdb_w500, outfile)

Generate Merge Table

Description

Generate Merge Table

Usage

generateMergeTable(txdb, minDistance = 200)

## S4 method for signature 'TxDb'
generateMergeTable(txdb, minDistance = 200L)

Arguments

txdb

an object representing a transcriptome
minDistance

the minimum separation to regard overlapping transcripts as unique

Value

a data.frame with three columns - tx_in the input transcript - tx_out the transcript merged into - gene_out the gene merged into

a data.frame with three columns - tx_in the input transcript - tx_out the transcript merged into - gene_out the gene merged into

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

## restrict to 'chrI' transcripts
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)
txdb_w500

## last 100 nts per tx
txdb_w100 <- truncateTxome(txdb, maxTxLength=100)
txdb_w100

Truncate Transcriptome

Description

Truncate Transcriptome

Usage

truncateTxome(txdb, maxTxLength = 500, ...)

## S4 method for signature 'TxDb'
truncateTxome(txdb, maxTxLength = 500, BPPARAM = bpparam())

Arguments

txdb

a TxDb object
maxTxLength

the maximum length of transcripts
...

additional arguments
BPPARAM

A BiocParallelParam object specifying whether and how the method should be parallelized.

Value

a TxDb object

a TxDb object

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

## restrict to 'chrI' transcripts
seqlevels(txdb) <- c("chrI")

## last 500 nts per tx
txdb_w500 <- truncateTxome(txdb)
txdb_w500

## last 100 nts per tx
txdb_w100 <- truncateTxome(txdb, maxTxLength=100)
txdb_w100

Convert TxDb object to GRangesList

Description

Convert TxDb object to GRangesList

Usage

txdbToGRangesList(
  txdb,
  geneCols = c("gene_id"),
  transcriptCols = c("gene_id", "tx_name"),
  exonCols = c("gene_id", "tx_name", "exon_id", "exon_rank")
)

Arguments

txdb

a TxDb object
geneCols

names of columns to include in the genes ranges
transcriptCols

names of columns to include in the transcripts ranges
exonCols

names of columns to include in the exons ranges

Value

a GRangesList object with entries c(genes, transcripts, exons)

Examples

library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)

## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene

grl <- txdbToGRangesList(txdb)
grl