filterByExpr {edgeR} | R Documentation

## Filter Genes By Expression Level

### Description

Determine which genes have sufficiently large counts to be retained in a statistical analysis.

### Usage

    ## S3 method for class 'DGEList'
    filterByExpr(y, design = NULL, group = NULL, lib.size = NULL, ...)
    ## S3 method for class 'SummarizedExperiment'
    filterByExpr(y, design = NULL, group = NULL, lib.size = NULL, ...)
    ## Default S3 method:
    filterByExpr(y, design = NULL, group = NULL, lib.size = NULL,
                 min.count = 10, min.total.count = 15, large.n = 10, min.prop = 0.7, ...)

### Arguments

`y` | matrix of counts, or a `DGEList` object, or a `SummarizedExperiment` object.
`design` | design matrix. Ignored if `group` is not `NULL`.
`group` | vector or factor giving group membership for a oneway layout, if appropriate.
`lib.size` | library size, defaults to `colSums(y)`.
`min.count` | numeric. Minimum count required for at least some samples.
`min.total.count` | numeric. Minimum total count required.
`large.n` | integer. Number of samples per group that is considered to be “large”.
`min.prop` | numeric. Minimum proportion of samples in the smallest group that express the gene.
`...` | any other arguments. For the `DGEList` and `SummarizedExperiment` methods, other arguments will be passed to the default method. For the default method, other arguments are not currently used.

### Details

This function implements the filtering strategy that was intuitively described by Chen et al (2016). Roughly speaking, the strategy keeps genes that have at least `min.count` reads in a worthwhile number samples. More precisely, the filtering keeps genes that have count-per-million (CPM) above k in n samples, where k is determined by `min.count` and by the sample library sizes and n is determined by the design matrix.

n is essentially the smallest group sample size or, more generally, the minimum inverse leverage of any fitted value. If all the group sizes are larger than `large.n`, then this is relaxed slightly, but with n always greater than `min.prop` of the smallest group size (70% by default).

In addition, each kept gene is required to have at least `min.total.count` reads across all the samples.

### Value

Logical vector of length `nrow(y)` indicating which rows of `y` to keep in the analysis.

### Author(s)

Gordon Smyth

### References

Chen Y, Lun ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. http://f1000research.com/articles/5-1438

### Examples

    ## Not run:
    keep <- filterByExpr(y, design)
    y <- y[keep,]

    ## End(Not run)

[Package edgeR version 3.34.1 Index]