DESeq2_FisherPvalue_Twopair: Combine P values for raw data with one input and two outputs

In zijinw/mmcc: R Functions used in McClelland Lab, University of California, Irvine

Description

This function is a variation of function DESeq2_FisherPvalue_Onepair. Now two different types of output are allowed.

Usage

DESeq2_FisherPvalue_Twopair(filepath, rawdatafile, num.in, num.out1, num.out2,
  name.out1 = "Input vs Output1", name.out2 = "Input vs Output2",
  name.out3 = "Output1 vs Output2")

Arguments

filepath	The path of the raw data (excluding the data file itself). Remember to double quote the filepath.
rawdatafile	The name of the raw data file. Remember to double quote the rawdatafile, and add the ".xlsx" after the name of rawdatafile (It must be excel file)!
num.in	The number of input columns in the raw data file.
num.out1	The number of output1 columns in the raw data file.
num.out2	The number of output2 columns in the raw data file.
name.out1	The prefix of "Input vs Output1" columns in the output file.
name.out2	The prefix of "Input vs Output2" columns in the output file.
name.out3	The prefix of "Output1 vs Output2" columns in the output file.
outputname.feature	The name of output file for each gene you want.
outputname.oligo	The name of output file for each oligo you want.

Details

This function should be used on a raw data with the following layout: 1. The first three columns must be "Feature", "Locus_Tag", "Strand" Here "Feture" can be barcode (preferred) or anything that unique. Be sure that the colnames are right! 2. The next columns are for input, output1, output2 successively. Note that there is no constraint for the names of these input and output columns, but there can only be 2 kinds of outputs. The number of columns in each output can be any number.

Examples

DESeq2_FisherPvalue_Twopair(filepath = "C:/Users/", rawdatafile = "rawdata.xlsx", outputname = "output", num.in = 3, num.out1 = 3, num.out2 = 3, name.out1 = "Input vs Output1", name.out2 = "Input vs Output2", name.out3 = "Output1 vs Output2")

zijinw/mmcc documentation built on May 4, 2019, 11:23 p.m.