subsetBy {MultiAssayExperiment} | R Documentation |
A set of functions for extracting and dividing a
MultiAssayExperiment
subsetByRow(x, y, ...) subsetByColData(x, y) subsetByColumn(x, y) subsetByAssay(x, y) ## S4 method for signature 'ExperimentList,ANY' subsetByRow(x, y, ...) ## S4 method for signature 'ExperimentList,list' subsetByRow(x, y) ## S4 method for signature 'ExperimentList,List' subsetByRow(x, y) ## S4 method for signature 'ExperimentList,logical' subsetByRow(x, y) ## S4 method for signature 'ExperimentList,list' subsetByColumn(x, y) ## S4 method for signature 'ExperimentList,List' subsetByColumn(x, y) ## S4 method for signature 'ExperimentList,logical' subsetByColumn(x, y) ## S4 method for signature 'ExperimentList' subsetByAssay(x, y) ## S4 method for signature 'MultiAssayExperiment,ANY' subsetByColData(x, y) ## S4 method for signature 'MultiAssayExperiment,character' subsetByColData(x, y) ## S4 method for signature 'MultiAssayExperiment,ANY' subsetByRow(x, y, ...) ## S4 method for signature 'MultiAssayExperiment,ANY' subsetByColumn(x, y) ## S4 method for signature 'MultiAssayExperiment' subsetByAssay(x, y) ## S4 method for signature 'MultiAssayExperiment,ANY,ANY,ANY' x[i, j, k, ..., drop = TRUE] ## S4 method for signature 'MultiAssayExperiment,ANY,ANY' x[[i, j, ...]] ## S4 replacement method for signature 'MultiAssayExperiment,ANY,ANY' x[[i, j, ...]] <- value ## S4 replacement method for signature 'MultiAssayExperiment,ANY,ANY,ANY' x[i, j, ...] <- value
x |
A |
y |
Any argument used for subsetting, can be a |
... |
Additional arguments passed on to lower level functions. |
i |
Either a |
j |
Either a |
k |
Either a |
drop |
logical (default TRUE) whether to drop empty assay elements
in the |
value |
An assay compatible with the MultiAssayExperiment API |
Subsetting a MultiAssayExperiment by the j index can yield a call
to either subsetByColData
or subsetByColumn
. For vector inputs,
the subset will be applied to the colData
rows. For List
-type
inputs, the List will be applied to each of the elements in the
ExperimentList
.
The order of the subsetting elements in the
List
must match that of the ExperimentList
in the
MultiAssayExperiment
.
subsetBycolData: Select biological units by vector input types
subsetByColumn: Select observations by assay or for each assay
subsetByRow: Select rows by assay or for each assay
subsetByAssay: Select experiments
## Load the example MultiAssayExperiment example("MultiAssayExperiment") ## Using experiment names subsetByAssay(mae, "Affy") ## Using numeric indices subsetByAssay(mae, 1:2) ## Using a logical vector subsetByAssay(mae, c(TRUE, FALSE, TRUE)) ## Subset by character vector (Jack) subsetByColData(mae, "Jack") ## Subset by numeric index of colData rows (Jack and Bob) subsetByColData(mae, c(1, 3)) ## Subset by logical indicator of colData rows (Jack and Jill) subsetByColData(mae, c(TRUE, TRUE, FALSE, FALSE)) subsetByColumn(mae, list(Affy = 1:2, Methyl450k = c(3,5,2), RNASeqGene = 2:4, GISTIC = 1)) subsetWith <- S4Vectors::mendoapply(`[`, colnames(mae), MoreArgs = list(1:2)) subsetByColumn(mae, subsetWith) ## Use a GRanges object to subset rows where ranged data present egr <- GenomicRanges::GRanges(seqnames = "chr2", IRanges::IRanges(start = 11, end = 13), strand = "-") subsetByRow(mae, egr) ## Use a logical vector (recycling used) subsetByRow(mae, c(TRUE, FALSE)) ## Use a character vector subsetByRow(mae, "ENST00000355076")