prep_data_for_SL: Prepare Dataset for SLIPT (Synthetic Lethal Predition)

Description Usage Arguments Examples

Description

Prepare data (e.g., gene expression data) for synthetic lethal prediction (typically count or continous data) by bining samples into categorical data for each gene to be tested.

Usage

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prep_data_for_SL(dataset, n = 3L, exclude = T)

Arguments

dataset

Dataset input to be formatted. Input is genes (rows) x samples (columns). Output data is transposed: samples (rows) x genes (columns).

n

number of quantiles to test. Must be an integer. Defaults to 3.

exclude

Do you wish to exclude genes without quartile variation? Defaults to TRUE.

Examples

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data <- c()
for(i in 1:100){
  data <- cbind(data, rnorm(1000))
}
rm(i)
rownames(data) <- paste("gene", 1:1000)
colnames(data) <- paste("sample", 1:100)
dim(data)

partitioned_data <- prep_data_for_SL(data, n = 3)
dim(partitioned_data)

TomKellyGenetics/slipt documentation built on May 8, 2019, 9:28 a.m.