castSE: castSE

In plger/SEtools: SEtools: tools for working with SummarizedExperiment

castSE

Description

Casts a data.frame as a SummarizedExperiment-class

Usage

castSE(
  x,
  rowNames = NULL,
  colNames = NULL,
  assayNames = NULL,
  colData = NULL,
  rowData = NULL,
  sparse = FALSE
)

Arguments

x	A data.frame
rowNames	Column of 'x' containing the row.names (if omitted, will build from 'rowData')
colNames	Column of 'x' containing the column names (if omitted, will build from 'colData')
assayNames	Columns of 'x' to turn into assays
colData	Columns of 'x' to use as colData
rowData	Columns of 'x' to use as rowData
sparse	Local, whether to keep the assays sparse.

Value

A SummarizedExperiment-class

Examples

d <- data.frame(transcript=rep(LETTERS[1:10],each=2), gene=rep(LETTERS[1:5],each=4),
                count=rpois(20, 10), sample=letters[1:2])
head(d)
castSE(d, rowData=c("transcript","gene"), colNames="sample")

plger/SEtools documentation built on Dec. 2, 2022, 3:58 p.m.