RunGscreend {gscreend} | R Documentation

## run gscreend

### Description

run gscreend

### Usage

    RunGscreend(object, quant1 = 0.1, quant2 = 0.9, alphacutoff = 0.05)

### Arguments

`object` | PoolScreenExp object
`quant1` | lower quantile for least quantile of squares regression (default: 0.1)
`quant2` | upper quantile for least quantile of squares regression (default: 0.9)
`alphacutoff` | alpha cutoff for alpha-RRA (default: 0.05)

### Value

object

### Examples

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

    # Create the PoolScreenExp to be analyzed
    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)

    pse <- createPoolScreenExp(se)

    # Run Analysis
    pse_an <- RunGscreend(pse)

[Package gscreend version 1.1.0 Index]