Linux

cnv calling R package [cn.mops] 설치하기

척척석사1 2022. 7. 24. 22:43

 

https://bioconductor.org/packages/release/bioc/html/cn.mops.html

 

cn.mops

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read cou

bioconductor.org

프로그램이 요구하는 R 버전과 required 패키지들을 갖춘 뒤 (없어도 cn.mops 설치하면서 같이 설치 됨 ! )

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cn.mops")

저기서 하라는대로 ..! BiocManager 설치 후 BiocManager 통해서 다운로드 받으면 손쉽게 ..! 받을 수 있다. 

install.packages("cn.mops") 도 해 봤는데 왜인지 R 버전 오류를 띄우더라고요. (R-4.1 기준)

 

설치가 잘 되었나 확인 해 보니 잘 되었다!

> library("cn.mops")
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘cn.mops’

The following object is masked from ‘package:S4Vectors’:

    params

 

반응형