read_rna_beatson: Read Beatson bed formatted RNA-Seq file
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles
Description
Usage
Arguments
Value
Author(s)
Description
read_rna_beatson reads a file containing promoter annotation data
together with gene expression levels from RNA-Seq experiments using the
fread function.
Usage
1
read_rna_beatson(file, chr_discarded = NULL, is_GRanges = TRUE)
Arguments
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.
Value
A GRanges object if is_GRanges is
TRUE, otherwise a data.table object.
The GRanges object contains three additional metadata columns:
-
id: IDs of each gene promoter.
-
gene_name: Gene name.
-
gene_fpkm: Expression level in
FPKM.
These columns can be accessed as follows:
granges_object$id
Author(s)
C.A.Kapourani C.A.Kapourani@ed.ac.uk
andreaskapou/BPRMeth-devel documentation built on May 12, 2019, 3:32 a.m.
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Description Usage Arguments Value Author(s)
Description
read_rna_beatson reads a file containing promoter annotation data
together with gene expression levels from RNA-Seq experiments using the
fread function.
Usage
1 | read_rna_beatson(file, chr_discarded = NULL, is_GRanges = TRUE)
|
Arguments
file |
The name of the file to read data values from. |
chr_discarded |
A vector with chromosome names to be discarded. |
is_GRanges |
Logical: if TRUE a GRanges object is returned, otherwise a data.frame object is returned. |
Value
A GRanges object if is_GRanges is
TRUE, otherwise a data.table object.
The GRanges object contains three additional metadata columns:
-
id: IDs of each gene promoter. -
gene_name: Gene name. -
gene_fpkm: Expression level in FPKM.
These columns can be accessed as follows:
granges_object$id
Author(s)
C.A.Kapourani C.A.Kapourani@ed.ac.uk
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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