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. |