Description
Usage
Arguments
Value
Author(s)
See Also
Examples
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
.
 ## S4 method for signature 'bcbioRNASeq,ANY,ANY,ANY'
x[i, j, = ]

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.

bcbioRNASeq
.
Lorena Pantano, Michael Steinbaugh
help("[", "base")
.
Other S4 Class Definition: bcbioRNASeq
,
coerce
, show
,
updateObject
1
2
3
4
5
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7
8
9
10
11
12
13
14
15
16  # Minimum of 100 genes, 2 samples
genes < ((), 100L)
(genes)
samples < ((), 2L)
(samples)
# Subset by sample name
, samples]
# Subset by gene list
[genes, ]
# Subset by both genes and samples
< [genes, samples]
()
assayNames()

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