Setting-up the model
Before you can run the actual comparison between groups you have to tell DiffBind how samples are split between them. The easiest way to do this is to use one of the predefined categories DiffBind attaches to the samples. These include commonly used groupings of interest like the condition or tissue associated with each sample. You can indicate which one you would like to use via the categories argument using constants like DBA_CONDITION and DBA_TISSUE. The help page for dba.contrast() has a complete list of the available constants.
This exercise is part of the course
ChIP-seq with Bioconductor in R
Exercise instructions
- Examine the
ar_bindingobject. - Identify the category corresponding to the Primary Tumor (primary) and Treatment Resistant (TURP) condition.
- Establish the contrast to compare the two tumor types.
- Examine the
dba_peaksobject to confirm that the contrast has been added.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Examine the ar_binding object
print(___)
# Identify the category corresponding to the tumor type contrast
contrast <- DBA____
# Establish the contrast to compare the two tumor types
dba_peaks <- dba.___(ar_binding, ___=contrast, minMembers=2)
# Examine the dba_peaks object to confirm that the contrast has been added
___(___)