Add Zero Timepoint Data to Treatment Subset

addZeroTime adds a zero timepoint to a specific treatment's data subset.

Usage

addZeroTime(data, condition, treat, zeroTreat, timeRange)

Arguments

data: A SummarizedExperiment object containing the experimental data.
condition: Character string corresponds to one of the columns from the colData of SE object.
treat: Character string specifying the treatment to which zero timepoint should be added.
zeroTreat: Character string specifying the treatment representing the zero timepoint.
timeRange: Character vector specifying the timepoints to include for the treatment.

Value

A SummarizedExperiment object with the zero timepoint added to the specified treatment's data.

Details

The function performs the following steps:

Subsets the data for the specified treatment and time range.
Subsets the data for the zero timepoint of the specified zero treatment.
Combines the assays from the treatment and zero timepoint subsets.
Updates the column data to reflect the combined treatment.
Returns a SummarizedExperiment object with the combined data.

Examples

library(SummarizedExperiment)
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# Load multiAssayExperiment object
data("dia_example")
# Get SummarizedExperiment object
se <- dia_example[["Phosphoproteome"]]
colData(se) <- colData(dia_example)
# Call the function
addZeroTime(se, condition = "treatment", treat = "EGF",
zeroTreat = "1stCrtl", timeRange = c("20min","40min", "6h"))
#> class: SummarizedExperiment 
#> dim: 500 6 
#> metadata(0):
#> assays(1): intensity
#> rownames(500): s1 s2 ... s499 s500
#> rowData names(7): UniprotID Gene ... Sequence site
#> colnames(6): FullProteome_EGF_0min_rep2 FullProteome_EGF_0min_rep3 ...
#>   FullProteome_EGF_0min_rep1 Phospho_EGF_0min_rep1
#> colData names(6): sample treatment ... sampleType sampleName