readTxResults {scater}R Documentation

Read transcript quantification data

Description

Create a SingleCellExperiment object from pseudo-aligner results via tximport.

Usage

readTxResults(..., full_length = TRUE)

readKallistoResults(..., full_length = TRUE)

readSalmonResults(..., full_length = TRUE)

Arguments

...

Arguments to be passed to tximport.

full_length

Logical scalar indicating whether the sequencing data is full-length (e.g., Smart-seq2) or end-biased, e.g., UMI-based protocols.

Details

If full_length=TRUE, counts are computed from the length-scaled TPMs. Otherwise, counts are not computed from the abundances.

readKallistoResults and readSalmonResults are simply wrappers around readTxResults with type pre-specified.

This function has now been deprecated in favour of tximeta. The latter produces a SummarizedExperiment that is easily coerced into a SingleCellExperiment.

Value

A SingleCellExperiment containing the abundance, count and feature length information from the supplied samples.

Author(s)

Davis McCarthy and Aaron Lun

References

Soneson C, Love MI, Robinson MD (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 4, 1521.

Examples

library(tximportData)
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("sample",1:6)
                        
# tx2gene links transcript IDs to gene IDs for summarization
tx2gene <- read.csv(file.path(dir, "tx2gene.gencode.v27.csv"))

sce <- readTxResults(files, type="salmon", tx2gene=tx2gene)

[Package scater version 1.10.1 Index]