# DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

## Documentation for package ‘DChIPRep’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

DChIPRep-package | DChIPRep: A package for differential analysis of histone modification ChIP-Seq profiles
chip_galonska | Another example ChIP data set that can be used with 'importDataFromMatrices' from rom Galonska et. al., 2015.
DChIPRep | DChIPRep: A package for differential analysis of histone modification ChIP-Seq profiles
DChIPRepResults | DChIPRepResults object and constructor
DChIPRepResults-class | DChIPRepResults object and constructor
DESeq2Data | Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults' object.
DESeq2Data-method | Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults' object.
DESeq2Data<- | Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults' object.
DESeq2Data<--method | Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults' object.
exampleChipData | An example ChIP data.
exampleInputData | An example input data.
exampleSampleTable | An example sample table data.frame
FDRresults | Accessor and setter for the 'FDRresults' slot of a 'DChIPRepResults' object.
FDRresults-method | Accessor and setter for the 'FDRresults' slot of a 'DChIPRepResults' object.
FDRresults<- | Accessor and setter for the 'FDRresults' slot of a 'DChIPRepResults' object.
FDRresults<--method | Accessor and setter for the 'FDRresults' slot of a 'DChIPRepResults' object.
getMATfromDataFrame | Helper function to turn a data.frame into a matrix and remove the ID column.
importData | Import the data after running the Python script
importDataFromMatrices | Import the data from ChiP and input matrices
importData_soGGi | Import the data from bam files directly
input_galonska | Another example Input data set that can be used with 'importDataFromMatrices' from rom Galonska et. al., 2015.
plotProfiles | Produce a TSS plot of the two conditions in the data
plotProfiles-method | Produce a TSS plot of the two conditions in the data
plotSignificance | Produce a plot that colors the positions identified as significant
plotSignificance-method | Produce a plot that colors the positions identified as significant
resultsDChIPRep | Accessors and setter for the 'results' slot of a 'DChIPRepResults' object.
resultsDChIPRep-method | Accessors and setter for the 'results' slot of a 'DChIPRepResults' object.
resultsDChIPRep<- | Accessors and setter for the 'results' slot of a 'DChIPRepResults' object.
resultsDChIPRep<--method | Accessors and setter for the 'results' slot of a 'DChIPRepResults' object.
robust_mean | Use a huber type estimator to produce a robust mean
runTesting | Run the tests on a DChIPRepResults object.
runTesting-method | Run the tests on a DChIPRepResults object.
sample_table_galonska | Another example sample table based on data from rom Galonska et. al., 2015.
show | prints the DESeq2Data slot of the DChIPRepResults object
show-method | prints the DESeq2Data slot of the DChIPRepResults object
summarizeCountsPerPosition | Helper function to summarize the counts per position
testData | A test DESeqDataSet
TSS_galonska | TSS around called peak regions from Galonska et. al.