export_SL_latex: An Export Function to process SLIPT predictions

In TomKellyGenetics/slipt: Synthetic Lethal Interaction Prediction Tool (SLIPT) from Cancer Genomics Data

Description

Exports the key synthetic lethal gene information in a LaTeX table. Can be done for all genes (output of detect_SL) or with synthetic lethal conditions and significance thresholds met (output of table_of_SL).

Usage

export_SL_latex(x)

Arguments

x	Data matrix. Synthetic Lethal predictions to process, typically the output of detect_SL or table_of_SL.

Examples

#prepare data
 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)
partitioned_data <- prep_data_for_SL(data, n = 3)

#run SLIPT
sl_table <- detect_SL("gene 1", partitioned_data)
dim(sl_table)
head(dim(sl_table))

sl_table <- detect_SL("gene 1", prep_data_for_SL(data))
dim(sl_table)
head(dim(sl_table))

#export top results to TeX
export_SL_latex(sl_table)

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