Upper-quartile/total-count normalization of raw sgRNA read count data

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Description

Apply the upper-quartile/total-count normalization to raw sgRNA read count data. In addition, this function can merge pairs of sgRNA read counts in different replications when CRISPR/Cas9 knockout screens are implemented with a few replications.

Usage

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UQnormalize(raw.count, trt, ctrl, round = TRUE, add.one = TRUE, print = FALSE)
TCnormalize(raw.count, trt, ctrl, round = TRUE, add.one = TRUE, print = FALSE)

Arguments

raw.count

A data.frame with raw sgRNA read counts. Rows represent sgRNAs and columns are the sgRNA names (1st), targeting gene names (2nd), and raw counts under multiple experimental conditions.

trt

A character vector of column names of raw.count corresponding to treatment conditions. Column names in the trt and ctrl vector should be paired.

ctrl

A character vector of column names of raw.count corresponding to control conditions.

round

Default is TRUE. If TRUE counts are rounded after setting the upper-quartile in each condition to be equal.

add.one

Default is TRUE. If TRUE this function adds one to all counts to make all the counts greater than or equal to one.

print

Default is FALSE. If TRUE it prints upper-quartiles of counts in different conditions before/after the normalization.

Value

Returns a data.frame with sgRNA name, targeting gene name and normalized counts under treatment and control.

See Also

sgRSEA