read_counts: Compute read counts

In leekgroup/recount: Explore and download data from the recount project

Compute read counts

Description

As described in the recount workflow, the counts provided by the recount2 project are base-pair counts. You can scale them using scale_counts or compute the read counts using the area under coverage information (AUC). We use the AUC because Rail-RNA soft clips some reads.

Usage

read_counts(rse, use_paired_end = TRUE, round = FALSE)

Arguments

rse	A RangedSummarizedExperiment-class object as downloaded with download_study.
use_paired_end	A logical vector. When TRUE it uses the paired-end flag (colData(rse)$paired_end) to determine whether the sample is paired-end or not. If it's paired-end, then it divides the counts by 2 to return paired-end read counts instead of fragment counts. When FALSE, this information is ignored.
round	Whether to round the counts to integers or not.

Details

Check the recount workflow for details about the counts provided by the recount2 project. Note that this function should not be used after scale_counts or it will return non-sensical results.

Value

Returns a RangedSummarizedExperiment-class object with the read counts.

Author(s)

Leonardo Collado-Torres

References

Collado-Torres L, Nellore A and Jaffe AE. recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor version 1; referees: 1 approved, 2 approved with reservations. F1000Research 2017, 6:1558 doi: 10.12688/f1000research.12223.1.

See Also

scale_counts

Examples

## Difference between read counts and reads downloaded by Rail-RNA
colSums(assays(read_counts(rse_gene_SRP009615))$counts) / 1e6 -
    colData(rse_gene_SRP009615)$reads_downloaded / 1e6

## Paired-end read counts vs fragment counts (single-end counts)
download_study("DRP000499")
load("DRP000499/rse_gene.Rdata")
colSums(assays(read_counts(rse_gene, use_paired_end = FALSE))$counts) /
    colSums(assays(read_counts(rse_gene))$counts)

## Difference between paired-end read counts vs paired-end reads downloaded
colSums(assays(read_counts(rse_gene))$counts) / 1e6 -
    colData(rse_gene)$reads_downloaded / 1e6 / 2

leekgroup/recount documentation built on May 24, 2024, 11:19 a.m.