README.md

In tengzhang123/m6A-express: Predicting context-specific m6A regulation of gene expression

m6A-express: Predicting context-specific m6A regulation of gene expression

m6A-express is a tool to identify m6A methylation significantly regulated expression genes in specific context

Pre-installing m6A-express

Before installing m6A-express package, user should have installed python 2.7 software in their platform (Windows systerm or Linux systerm). And some python packages should be installed, such as numpy, statsmodels.api, pandas, scipy.

Installation Instructions

The m6A-express package can be installed by the following R commands:

devtools::install_github("tengzhang123/m6A-express")

library(m6A-express)

Usage Example

The following command code will show how to use this package and output m6A methylation regulated expression gene in excel files

Basic mode: pooled samples from one or multiple conditions together and identify m6A regulated expression gene in a specific context.

Input BAM files.

f1 <- system.file("extdata", "IP1.bam", package="m6A-express")

f2 <- system.file("extdata", "IP2.bam", package="m6A-express")

f3 <- system.file("extdata", "IP3.bam", package="m6A-express")

f4 <- system.file("extdata", "IP4.bam", package="m6A-express")

f5 <- system.file("extdata", "Input1.bam", package="m6A-express")

f6 <- system.file("extdata", "Input2.bam", package="m6A-express")

f7 <- system.file("extdata", "Input3.bam", package="m6A-express")

f8 <- system.file("extdata", "Input4.bam", package="m6A-express")

IP_BAM <- c(f1,f2,f3,f4)

INPUT_BAM <- c(f5,f6,f7,f8)

We use GTF file in the following example.

gtf <- system.file("extdata", "hg19toy.gtf", package="m6A-express")

Predict m6A regulated expression gene by m6A-express model

m6A_reg_exp_gene <- m6A_express(express_data=INPUT_BAM, IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM, annot_type="hg19", GENE_ANNO_GTF=gtf, pvalue=0.05,mode="basic")

DE-DM mode: In this case, we will detect whether the differential m6A methylation peak sites regulated expression that caused the differential expression genes

Predict the differential expression genes are regulated by differential methylation peak sites by m6A-express model

IP_BAM <- c(f1,f2)

TREATED_IP_BAM <- c(f3,f4)

INPUT_BAM <- c(f5,f6)

TREATED_INPUT_BAM <- c(f7,f8)

m6A_reg_exp_gene <- m6A_express(express_data=INPUT_BAM, treated_express_data=TREATED_INPUT_BAM, IP_BAM=IP_BAM, TREATED_IP_BAM=TREATED_IP_BAM, INPUT_BAM=INPUT_BAM, TREATED_INPUT_BAM=TREATED_INPUT_BAM,annot_type="hg19", GENE_ANNO_GTF=gtf,pvalue=0.05,mode="DE-DM")

tengzhang123/m6A-express documentation built on Aug. 15, 2020, 7:01 a.m.