subset: Bracket-Based Subsetting

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Extract genes by row and samples by column from a bcbioRNASeq object. The internal DESeqDataSet and count transformations are rescaled automatically. DESeq2 transformations can be disabled on large subset operations by setting transform = FALSE.

Usage

## S4 method for signature 'bcbioRNASeq,ANY,ANY,ANY'
x[i, j, drop = FALSE]

Arguments

x	object from which to extract element(s) or in which to replace element(s).
i	indices specifying elements to extract or replace. Indices are numeric or character vectors or empty (missing) or NULL. Numeric values are coerced to integer as by as.integer (and hence truncated towards zero). Character vectors will be matched to the names of the object (or for matrices/arrays, the dimnames): see ‘Character indices’ below for further details. For [-indexing only: i, j, ... can be logical vectors, indicating elements/slices to select. Such vectors are recycled if necessary to match the corresponding extent. i, j, ... can also be negative integers, indicating elements/slices to leave out of the selection. When indexing arrays by [ a single argument i can be a matrix with as many columns as there are dimensions of x; the result is then a vector with elements corresponding to the sets of indices in each row of i. An index value of NULL is treated as if it were integer(0).
j	indices specifying elements to extract or replace. Indices are numeric or character vectors or empty (missing) or NULL. Numeric values are coerced to integer as by as.integer (and hence truncated towards zero). Character vectors will be matched to the names of the object (or for matrices/arrays, the dimnames): see ‘Character indices’ below for further details. For [-indexing only: i, j, ... can be logical vectors, indicating elements/slices to select. Such vectors are recycled if necessary to match the corresponding extent. i, j, ... can also be negative integers, indicating elements/slices to leave out of the selection. When indexing arrays by [ a single argument i can be a matrix with as many columns as there are dimensions of x; the result is then a vector with elements corresponding to the sets of indices in each row of i. An index value of NULL is treated as if it were integer(0).
drop	For matrices and arrays. If TRUE the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement. See drop for further details.

Value

bcbioRNASeq.

Author(s)

Lorena Pantano, Michael Steinbaugh

See Also

help("[", "base").

Other S4 Class Definition: bcbioRNASeq, coerce, show, updateObject

Examples

# Minimum of 100 genes, 2 samples
genes <- head(rownames(bcb_small), 100L)
head(genes)
samples <- head(colnames(bcb_small), 2L)
head(samples)

# Subset by sample name
bcb_small[, samples]

# Subset by gene list
bcb_small[genes, ]

# Subset by both genes and samples
subset <- bcb_small[genes, samples]
print(subset)
assayNames(subset)

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.