R包 viRome

viRome包

功能介绍：

We have developed code in R to analyse short-read next-generation sequencing data from virus-infection studies where the siRNA or piRNA pathways have been implicated.  The package provides a range of functions to help scientists visualise the results of such experiments.

结果展示：

viRome包 结果展示

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官方网址:

http://www.arkgenomics.org/bioinformatics/virome

运行手册:

1、安装

# get the necessary Bioconductor packages

source("http://www.bioconductor.org/biocLite.R")

biocLite("Rsamtools")

# install optional Bioconductor packages

# biocLite("seqLogo")

# biocLite("motifStack")

# install the necessary R packages

install.packages(c("plyr","gsubfn","seqinr","reshape2"))

# install optional R packages

# install.packages("ggplot2")

2、使用

# load the library

# find example data

library(viRome)

infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")

# minimal commands

bam    <- read.bam(infile, chr="SINV") # requires the full path to a bam file, and the name of the reference the data are aligned to

bamc   <- clip.bam(bam)                # requires only the output of read.bam()

bpl    <- barplot.bam(bamc)            # requires only the output of clip.bam()

ssp    <- size.strand.bias.plot(bpl)   # requires only the output of barplot.bam()

dm     <- summarise.by.length(bamc)    # requires only the output of clip.bam()

sph    <- size.position.heatmap(dm)    # requires only the output of summarise.by.length()

sbp    <- stacked.barplot(dm)          # requires only the output of summarise.by.length()

sir    <- position.barplot(bamc) 

# requires only the output of clip.bam(), though one should alter minlen, maxlen and reflen

sr     <- sequence.report(bamc)        # requires only the output of clip.bam()

pwm    <- make.pwm(bamc)               # requires only the output of clip.bam()

pmh    <- pwm.heatmap(pwm)             # requires only the output of make.pwm()

rdp    <- read.dist.plot(sr)           # requires only the output of sequence.report()

3、注意事项

读入数据的时候，system.file输入的是包内部的路径。

1、可以不用system.file方法，自己写路径

2、或者用system.file()找到路径，把自己的数据拷贝进去

infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")

bam    <- read.bam(infile, chr="SINV") 

# requires the full path to a bam file, and the name of the reference the data are aligned to​

3、需要为bam文件排序建索引，然后全都拷贝到路径里

samtools view -bS result.sam -o result.bam 

#sam转bam文件

samtools sort result.bam -o result.sorted

#排序

samtools index result.sorted

#建立索引​

具体详情：

参考官网优先：

http://www.arkgenomics.org/bioinformatics/virome

在R中用 ?方法名 查看具体用法