Cas9 Knockout Screen Data

Description Usage Arguments Value See Also

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.

1 2	UQnormalize(raw.count, trt, ctrl, round = TRUE, add.one = TRUE, print = FALSE) TCnormalize(raw.count, trt, ctrl, round = TRUE, add.one = TRUE, print = FALSE)

`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.