Get_expression: Obtained the reads count of each gene by Rsubread

In NWPU-903PR/m6Aexpress: Predicting context-specific m6A regulation of gene expression

Description

This founction is to obtained gene reads count by Rsubread given Gene Anotation File (GTF) or in-built annotation.

Usage

Get_express_data(INPUT_BAM, 
                 TREATED_INPUT_BAM=character(0),
                  species="human",
                  annot_file="hg19",
                  isPairedEnd=FALSE,
                  GENE_ANNO_GTF = NULL,
                  isGTFAnnotationFile=FALSE
                  )

Arguments

INPUT_BAM	a character vector giving names of INPUT samples in MeRIP-seq data, which specifies a path for allignment reads in BAM format.
TREATED_INPUT_BAM	a character vector giving names of treated INPUT samples in MeRIP-seq data, which specifies a path for allignment reads in BAM format. These files are only provided in differential methylation context.
annot_file	a character string specifying an in-built annotation used to quantify each gene's reads count for expression data. It has four possible values including "mm10", "mm9", "hg38" and "hg19", corresponding to the NCBI RefSeq annotations for genomes ‘mm10’, ‘mm9’, ‘hg38’ and ‘hg19’, respectively. "hg19" by default.
species	a character string specifying the name of species, which could be "human", "mouse". This parameter is only appliable when GENE_ANNO_GTF is NULL.
GENE_ANNO_GTF	A character string giving name of a user-provided annotation file in GTF format. Note that GENE_ANNO_GTF will override annot_type if both provided.
isGTFAnnotationFile	logical indicating whether the annotation provided via the annot_type argument is in GTF format. FALSE by default. This option is only applicable when GENE_ANNO_GTF is not NULL.
isPairedEnd	logical indicating if counting should be performed on read pairs or reads. FALSE by default. If TRUE, read pairs will be counted instead of individual reads.

Details

Get_expression_data is a general-purpose read summarization function that can assign mapped reads from RNA sequencing to genomic features (gene).

The function takes as input a set of BAM files containing read mapping results.

Get_expression_data accepts GTF/GFF annotation formats or in-built annotation for human "hg19", "hg38" or mouse muscle "mm9" or "mm10".

Value

Get_expression_data will return a list data format, which includes a dataframe with reads count for each gene in each INPUT sample and a vector of size factor for each INPUT sample whose columans.

gene_reads_count	A dataframe format, which includes the reads count for each gene in each INPUT sample.
size_factor	A vector in float type, which are used to normalize samples.

References

Yang Liao, Gordon K Smyth and Wei Shi (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research, 47(8):e47. http://www.ncbi.nlm.nih.gov/pubmed/30783653

See Also

featureCounts

Examples

## Not run: 
##Get gene expression data for each INPUT BAM file.
f1 <- system.file("extdata", "Input1.bam", package="m6Aexpress")
f2 <- system.file("extdata", "Input2.bam", package="m6Aexpress")
f3 <- system.file("extdata", "Input3.bam", package="m6Aexpress")
f4 <- system.file("extdata", "Input4.bam", package="m6Aexpress")
INPUT_BAM <- c(f1,f2,f3,f4)
# Input the annotation file
gtf <- system.file("extdata", "hg19toy.gtf", package="m6Aexpress")
# Get reads count for each gene of each sample by given GTF file.
get_gene_express <- Get_express_data(INPUT_BAM=INPUT_BAM, 
                                      isPairedEnd=FALSE,
                                      GENE_ANNO_GTF = gtf)
## Not run:                                      
# Get reads count for each gene of each sample by in-built annotation file.
# get_gene_express <- Get_express_data(INPUT_BAM=INPUT_BAM, 
                                      species="human",
                                      annot_file="hg19",
                                      isPairedEnd=FALSE,
                                     GENE_ANNO_GTF = NULL,
                                    isGTFAnnotationFile=FALSE) 

## End(Not run)
      

NWPU-903PR/m6Aexpress documentation built on Dec. 17, 2021, 5:18 a.m.