createPoolScreenExp: Create PoolScreenExp Experiment

In gscreend: Analysis of pooled genetic screens

Description

Create PoolScreenExp Experiment

Usage

createPoolScreenExp(data)

Arguments

data	Input data object containing gRNA level data (SummarizedExperiment)

Value

object PoolScreenExp object

Examples

raw_counts <- read.table(
                        system.file('extdata', 'simulated_counts.txt',
                        package = 'gscreend'),
                        header=TRUE)

counts_matrix <- cbind(raw_counts$library0, raw_counts$R0_0, raw_counts$R1_0)

rowData <- data.frame(sgRNA_id = raw_counts$sgrna_id,
gene = raw_counts$Gene)

colData <- data.frame(samplename = c('library', 'R1', 'R2'),
timepoint = c('T0', 'T1', 'T1'))

library(SummarizedExperiment)
se <- SummarizedExperiment(assays=list(counts=counts_matrix),
rowData=rowData, colData=colData)

# create a PoolScreenExp experiment
pse <- createPoolScreenExp(se)

gscreend documentation built on Nov. 8, 2020, 7:18 p.m.