screenProcessing: screenProcessing function

In cherkaos/CRISPRScreenProcessing: Processing function to identify gRNA in CRISPR organoid screen

screenProcessing function

Description

screenProcessing function

Usage

screenProcessing(
  inputfile,
  controlStart,
  controlEnd,
  resultfile,
  maxsgRNA,
  minReadCount,
  zscore,
  orderOutput = TRUE,
  shortOutput = TRUE
)

Arguments

inputfile	Input file name. File must contains clones/organoids in the columns and sgRNAs in the rows. First row are the clones/organoids names and the two first column are the sgRNAs name and IDs. Control clones/organoids should be placed at the beginning/left of the file and unknown clones/organoids subsequently. File can be a csv or txt a file (comma separated) located in the working directory.
controlStart	Name of first control clone/organoid in inputfile. The name should match the column name and should not contain special characters.
controlEnd	Name of last control clone/organoid in inputfile. The name should match the column name and should not contain special characters.
resultfile	Output file name.
maxsgRNA	Maximum number of integrated sgRNAs per clone/organoid.
minReadCount	Minimum read count to consider a sgRNA.
zscore	Logical value indicating if the read counts should be zscore for each clones/organoids.
orderOutput	Logical value indicating if clones should be ordered by the number of integrated sgRNAs in the output file.
shortOutput	Logical value indicating if all sgRNAs (e.g. the non integrated one) should be included in the output file.

Value

resultfile

Examples

print("Examples")

cherkaos/CRISPRScreenProcessing documentation built on June 12, 2022, 1:02 p.m.