annotat: Annotation of genes within which alternative splicing occurs

In NBBttest: Negative Binomial Beta t-Test

Annotation of genes within which alternative splicing occurs

Description

Alternative splicing is detected in any element of 3'UTR, 5'UTR, exons and introns within a gene using RNA-seq data where RNA reads are mapped to a reference genome. As an example for annotation, the RNA-seq reads derived from human samples can be mapped onto human genome reference (GRCh38) using different methods, for example, HTSeq, spladder, rMAT, cufflinks, etc. These methods can detect alternative splicing sites within genes. However, none of these methods does gene annotation for users. Our NBBttest offers a R function for annotating genes with exons or isoforms.

Usage

annotat(infile, mfile, type="gene", colunmset = "NLL")

Arguments

infile	input data file with ENSGid column for annotation
mfile	reference genome file with ENSG id column.
type	has three options: "gene", "isoform" or ""isof" and "exon", see details. The default is "gene".
colunmset	EGNSid column set. If the RNA count data are made by using HTSeq and DEXSeq annotation file, then some of genes have many different ENSGids. For example, ENSG00000285476+ENSG00000182230+ENSG00000251623 has three ENSG ids ENSG00000285476,ENSG00000182230, and ENSG00000251623 that share one gene, so it is splited into three columns (2,3,4)in excel. The default is 2(column 2).

Details

If type = "gene", then count data of RNA reads are obtained at gene level, annotation would be executed at gene level or if type = "isof" or "isoform", then RNA reads were mapped onto elements (for example, 3'UTR, 5'UTR, exon or cassette, intron) within genes and annotation would be executed at isoform level or if type = "exon", then RNA count data were obtained by mapping RNA reads onto exome by DEXseq and annotation would be done at exon level defined by DEXSeq. Note that GRCh38 is too big so it was removed from data. User may request to get it from yuande/github.

Value

return original data with an additional column for gene.

Author(s)

Yuan-De Tan [e-mail]

Examples

data(DDX39_100)
data(gtfa)
DDX39_30<-annotat(infile=DDX39_100[1:30,],mfile=gtfa,type="gene")

NBBttest documentation built on May 30, 2022, 1:05 a.m.