getTagMatricesForDiffExpLevelBins: getTagMatricesForDiffExpLevelBins

In WilliamSalvidge/dictyChipSeq: What the Package Does (One Line, Title Case)

getTagMatricesForDiffExpLevelBins

Description

Takes in a list of dataframes. Was desgined to take in the different expression dataframes that are the output go makeAx4TPM(). It will then subset the GRanges object within the csAnno object anno slot and perform the tagMatrix generation on just that subset.

Usage

getTagMatricesForDiffExpLevelBins(x = NULL, y, z)

Arguments

x	list of dataframes based on gene expression
y	csAnno Object. OR if x is NULL a GRanges object.
z	GRanges object of dicty promoters

Details

This is actually a badly written function! When you subset based on the geneID annotation associated with high, medium or low expression you do return GRanges objects that contain peaks that have been assigned to high, medium or lowly expressed genes, HOWEVER! getTagMatrix doesn't care that each peak has only been assigned to 1 geneID. It just looks to see if that peak overlaps with the promoters of any genes and then returns that in the tagMatrix. In the following functions we go in and take out any incorrect coverage!

Each call to getTagMatrixWill will generate a Windows GRange with an index attached. Worthwhile checking that are all identical. all(start(testGetTagMats$Genes_1_to_1042$Windows) == start(testGetTagMats$Genes_1042_to_2082$Windows)) << maybe use to compare.

It can also just accept a GRanges object in the y paramter in which case the output will contain only 1 tagMatrix and windows.

Value

Output is a list with tagMatrices based on expression and Windows of promoters

WilliamSalvidge/dictyChipSeq documentation built on March 28, 2023, 1:27 a.m.