read_rna_encode_caltech: Read ENCODE Caltech bed formatted RNA-Seq file
In andreaskapou/processHTS: Process HTS Files and Data

Description Usage Arguments Value Author(s) See Also Examples

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.

1	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 four additional metadata columns:

ensembl_id: Ensembl IDs of each gene promoter.
gene_name: Gene name.
gene_expr: Expression level in the format required by ENCODE.
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

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# Get the location of the RNA-Seq file
rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "processHTS")
rna_data <- read_rna_encode_caltech(file=rnaseq_file, is_GRanges=FALSE)