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

Documentation for package ‘DChIPRep’ version 1.8.0

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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.