R Code for Focused shRNA Screening Analysis

Authors

David Oliver, Piaomu Liu, and Edsel Peña

shRNA_Screening_Analysis.r requires:

• MASS
• reshape2
• preprocessCore (bioconductor)

shRNA_Screening_Analysis.r "install":

git clone https://github.com/doliv071/Focused_shRNA_Analysis.git

In R, source the file

source(shRNA_Screening_Analysis.r)

shRNA_Screening_Analysis.r usage:

Run the function

shRNA_Screening_Analysis()

required parameters:

• dat1 = "control.csv" # Control data
• dat2 = "treat.csv" # Treated data
• genes = "targets.txt" # List of genes with targeting shRNAs, 1 per line

**NOTE**: data files must be csv

**NOTE**: rownames for the data must be gene-specific shRNA names that match the gene names specified by targets.txt. (e.g. For 3 shRNAs targeting RPL35A, the rownames should be RPL35A1, RPL35A2, RPL35A3)

Additional parameters that can be specified:

• BootRep = 10000 # Number of boot strap repetitions
• thresh = 10 # Minimum number of shRNA reads to include in analysis. shRNAs with less than the threshold number of counts are converted to NA
• passages = 5 # Number of passages (could be rounds of any sort of selection)
• bio.reps = 2 # Number of biological replicates
• adjust = "BH" # Method to use for adjusting p-value for multiple testing. Argument is passed to p.adjust{stats}. see ?p.adjust for available options.