batchLookUp: Combines results of multiple screens in single dataframe

In Tsvanemden/sgaMethods: Analyzes SGAs

Description

Based on a sample table, extracts results of screens out of the .txt file generated by batchScreenAnalysis and combines them into a single datafame.

Usage

batchLookUp(x, nameOutput, interest, genelist, threshold = 100)

Arguments

x	A dataframe containing info on each screen that needs to be added to the final dataframe.
nameOutput	Name of the output dataframe that will added to your global environment.
interest	Indicates in which batchScreenAnalysis column you are interested in. Chose between "ratio" and "MEDnorm".
genelist	List of all genes you want to have in you final data frame.
threshold	Selects minimal pixels size for first media. Default is 100

Value

genelist

Examples

    # Define sample table
    location_results <- c("/Desktop/screen1","/Desktop/screen2","/Desktop/screen3")
    screen_name <- c("screen1","screen2","screen3")
    type <- c("mat","mat","tel")
    mutant <- c("wt","abc","wt")
    assay_stress <- c("std","std","temp")
    media1 <- c("NS","NS","NS")
    media2 <- c("URA","URA","URA")
    sampleTable <- data.frame(location_results, screen_name, type, mutant, assay_stress, media1, media2)
    # Genes you are interested in
    genelist <- c("abc","def","ghi", "jkl","mno","oqr")
    # Call the function
    batchLookUp(sampleTable, "screen.df", "ratio", genelist, threshold = 150)

Tsvanemden/sgaMethods documentation built on May 7, 2019, 8:24 a.m.