| read_rna_encode_caltech {BPRMeth} | R Documentation |
(DEPRECATED) read_rna_encode_caltech reads a file
containing promoter annotation data together with gene expression levels
from RNA-Seq experiments using the scan function. The RNA-Seq
file should be in ENCODE Caltech bed format, e.g. use gtf2bed
tool if your initial file is in gtf format.
read_rna_encode_caltech(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 three additional metadata columns:
ensembl_id: Ensembl IDs of each gene promoter.
gene_name: Gene name.
gene_fpkm: Expression level in
FPKM.
These columns can be accessed as follows:
granges_object$ensembl_id
C.A.Kapourani C.A.Kapourani@ed.ac.uk
read_chrom_size, read_bs_encode_haib
# Obtain the path to the file and then read it
rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "BPRMeth")
rna_data <- read_rna_encode_caltech(rnaseq_file)