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


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Documentation for package ‘DChIPRep’ version 1.4.0

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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.
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.