Description Usage Arguments Value Important Author(s) References See Also Examples
read_bs_bismark_cov
reads a file containing methylation data from
BS-Seq experiments using the fread
function. The
BS-Seq file should be in Bismark Cov format. Read the Important section below
on when to use this function.
1 | read_bs_bismark_cov(file, chr_discarded = NULL, is_GRanges = TRUE)
|
file |
The name of the file to read data values from. |
chr_discarded |
A vector with chromosome names to be discarded. |
is_GRanges |
Logical: if TRUE a GRanges object is returned, otherwise a data.frame object is returned. |
A GRanges
object if is_GRanges
is
TRUE, otherwise a data.table
object.
The GRanges object contains two additional metadata columns:
total_reads
: total reads mapped to each genomic location.
meth_reads
: methylated reads mapped to each genomic location.
These columns can be accessed as follows:
granges_object$total_reads
Unless you want to create a different workflow when
processing the BS-Seq data, you should NOT call this function, since this
is a helper function. Instead you should call the
preprocess_bs_seq
function.
C.A.Kapourani C.A.Kapourani@ed.ac.uk
http://rnbeads.mpi-inf.mpg.de/data/RnBeads.pdf
pool_bs_seq_rep
, preprocess_bs_seq
1 2 3 | # Get the location of the bismark file
bism_file <- system.file("extdata", "bism_rep1.bed", package = "processHTS")
bs_data <- read_bs_bismark_cov(file = bism_file, is_GRanges = TRUE)
|
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