screenProcessing: screenProcessing function

Description Usage Arguments Value Examples

View source: R/screenProcessing.R

Description

screenProcessing function

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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

1
print("Examples")

cherkaos/CRISPRScreenProcessing documentation built on Jan. 22, 2020, 9:14 p.m.