peak_calling: Peak calling based on 'exomePeak2' for MeRIP-seq dataset

In NWPU-903PR/m6AexpressBHM: m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

Peak calling based on exomePeak2 for MeRIP-seq dataset

Description

peak_calling conducts peak calling and peak statistics calculation from BAM files of a MeRIP-seq experiment.

1. Check and index the BAM files with scanMeripBAM.

2. Call modification peaks on exons with exomePeakCalling.

3. Estimate sequencing depth size factors for each MeRIP-seq samples exomePeakCalling.

4. Calculate offset factors of GC content biases with estimateSeqDepth.

5. Calculate (differential) modification statistics with the generalized linear model (GLM) using glmM.

6. Export the peaks/sites statistics with user defined format by exportResults.

Usage

peak_calling(IP_BAM = NULL,
             INPUT_BAM = NULL,
             GENE_ANNO_GTF = NULL,
             paired_end = FALSE,
             Genome = NA,
             output_dir)

Arguments

IP_BAM	a character vector for the BAM file directories of the IP samples.
INPUT_BAM	a character vector for the BAM file directories of the Input samples.
GENE_ANNO_GTF	a character specifies the directory toward a gene annotation GFF/GTF file.
Genome	a BSgenome object for the genome sequence information. For example: Genome = "hg19".
output_dir	a character for the name of the directory being output; Default = "exomePeak2_output".

Details

peak_calling call RNA modification peaks and calculate peak statistics from BAM files of a MeRIP-seq experiment based on exomePeak2 R package.

The transcript annotation from the GFF file) should be provided to perform analysis on exons.

The BSgenome object is also required to perform the GC content bias adjustment. If the Genome argument is not provided (= NULL), the downstream analysis will proceed without GC content bias corrections.

Under the default setting, peak_calling will save the results of modification analysis under a folder named 'exomePeak2_output'. The results generated include a BED file and a CSV table that stores the locations and statistics of the modified peaks/sites. peak_calling also report the sequencing depth size factors for each MeRIP-seq samples, which are save in the same output directory in a "size_factor.Rdata" file

See Also

See Also as ?exomePeak2

Examples

## Not run: 
library(exomePeak2)
f1 <- "./group1_IP1.bam"
f2 <- "./group1_IP2.bam"
f3 <- "./group1_IP3.bam"
f4 <- "./group1_Input1.bam"
f5 <- "./group1_Input2.bam"
f6 <- "./group1_Input3.bam"
group1_IP_BAM <- c(f1,f2,f3)
group1_INPUT_BAM <- c(f4,f5,f6)
GENE_ANNO_GTF = "./hg19_GTF/genes.gtf"
###peak calling for group1
group1_peak_calling <- peak_calling(IP_BAM=group1_IP_BAM,
                                    INPUT_BAM=group1_INPUT_BAM,
                                    GENE_ANNO_GTF=GENE_ANNO_GTF,
                                    paired_end = FALSE,
                                    Genome = "hg19"
                                    output_dir="./Group1_peakcalling")

## End(Not run)

NWPU-903PR/m6AexpressBHM documentation built on May 29, 2022, 11:07 p.m.