Additional package to extend the data read by Haplin.
The HaplinMethyl package provides three categories of important functions:
- reading the data,
- loading the read-in data, and
- manipulating the environmental data.
The two functions (envDataRead and envDataReadFromObj) read in
the data and create an object of env.data class, which is
a list of ff-matrices. Simultaneously, two files are written: .RData
and .ffData. These are connected and will be used in the data-loading
function. The object created here has also summary and print
methods defined for easier viewing.
envDataLoad function loads the data, which is super-fast, compared to
reading the data in.
The user can extract a subset of the data read in by any of the above
functions, with envDataSubset. This will create new .RData and
.ffData files. Moreover, there are two functions that are created
specifically for DNA methylation data: findCpGsnearSNP and
findCpGsRange can be used to create CpG lists that are near a given
SNP or within a certain coordinate range.
Checkout the vignettes!
vignette(package = "HaplinMethyl")
If you don't have devtools installed, run
install.packages("devtools")
Then, you're ready to install the newest HaplinMethyl via
devtools::install_github("jromanowska/HaplinMethyl")