makeTimeSeriesExperimentFromExpressionSet: TimeSeriesExperiment constructor from ExpressionSet

In nlhuong/vistimeseq: Analysis for short time-series data

Description

TimeSeriesExperiment constructor initializes the TimeSeriesExperiment object from ExpressionSet and populates the time, replicate, and group slots.

Usage

makeTimeSeriesExperimentFromExpressionSet(
  eset,
  timepoint = NULL,
  group = NULL,
  replicate = NULL
)

Arguments

eset	ExpressionSet object
timepoint	a vector indicating timepoint at which each sample was collected or a character string equal to one of the column names of a supplied ExpressionSet.
group	a vector indicating a group membership for each sample or a character string equal to one of the column names of a supplied ExpressionSet If not specified, the group is set to 'G1' for each sample.
replicate	a vector indicating a replicate id of each sample or a character string equal to one of the column names of a supplied ExpressionSet If not specified, the replicate is set to 'R1' for each sample.

Details

TimeSeriesExperiment is an extension of SummarizedExperiment class.

Value

Returns an initialized TimeSeriesExperiment object.

Examples

raw <- matrix(runif(3000), ncol = 30)
pheno.data <- data.frame(
   time = rep(rep(1:5, each = 3), 2),
   replicate = rep(1:3, 10),
   group = rep(1:2, each = 15))
feature.data <- data.frame(
   feature = paste0("F", 1:100)
)
## Not run: 
    library(Biobase)
    test_eset <- ExpressionSet(
         raw, phenoData = AnnotatedDataFrame(pheno.data),
         featureData = AnnotatedDataFrame(feature.data))
    test_TimeSeriesExperiment <- makeTimeSeriesExperimentFromExpressionSet(
       test_eset, timepoint = "time", group = "group",
       replicate = "replicate")
    test_TimeSeriesExperiment

## End(Not run)

nlhuong/vistimeseq documentation built on Sept. 4, 2021, 2:41 a.m.