【工具】grcMalaria用于处理和分析“斑点疟疾基因报告卡”的R软件包

文章目录

介绍

grcMalaria 是一个易于使用的、开源的 R 软件包,旨在使遗传流行病学分析任务变得易于操作。

该软件包能够将来自"SpotMalaria 遗传报告卡"(GRC)中提取的疟原虫遗传信息转化为直观的流行率、多样性、亲缘关系等地理图谱。该软件库还能够识别流行毒株、分析药物耐药性特征以及绘制传播路径。

grcMalaria is a user-friendly, open-source R package, designed to make genetic epidemiology analysis tasks accessible.
The package facilitates the translation of genetic information derived from malaria parasites from SpotMalaria Genetic Report Cards (GRC) into intuitive geographical maps of prevalence, diversity, relatedness. This software library is also capable of identifying circulating strains, characterising drug resistance profiles, and mapping spread.

代码

https://genremekong.org/tools/grcmalaria-guide

r 复制代码
## Install devtools and rgeos
install.packages("devtools")
install.packages("rgeos")

##Install grcMalariaGeodata from Github
devtools::install_github("malariagen/grcMalariaGeodata")

## Require these dependencies to install 'malariagen/grcMalaria'
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("pcaMethods")

# Load libraries
library(grcMalariaGeodata)
library(grcMalaria)

# Check package versions grcMalaria and grcMalariaGeodata
# Latest version grcMalariaGeodata: 0.4.0
# Latest stable version of grcMalaria: 2.0.0
packageVersion('grcMalaria')
packageVersion('grcMalariaGeodata')


# Load data file
# Change the path to where your file is located before running the code
Data <- loadGrc("D:/.../GRC.xlsx", 
    sheet = "GenRe-Mekong", 
    species = "Pf", version = "1.4")

ctx <- initializeContext(Data, 
                          dir="D:/...", #Change the path to where you want output file to be 
															 minSnpTypability=0.8, minSampleTypability=0.75) 


## Select sample set to work on. 

# To select samples from 1 field (1 column in the GRC)
selectSampleSet(ctx, sampleSetName="EBKK", select=list(
								list(field="Country", values=c("VN", "KH", "LA")) ))

# To select samples from 2 fields
selectSampleSet(ctx, sampleSetName="Laos", select=list(
								list(field="TimePoint", values=c("D00H00","-")),
								list(field="Study", values=c("1208-PF-LA-CMPE-GENRE")) ))

# To select samples from 3 fields
selectSampleSet(ctx, sampleSetName="SouthLA_2017", select=list(
                 list(field="Country", values="LA"),
                 list(field="AdmDiv1", values=c("Attapeu", "Champasak")),
								 list(field="Year", values=c("2017", "2018")) ))

# To select samples from more fields, follow the example above to add more -> list(field=" ", values = " ")


mapSampleCounts (ctx, sampleSet="EBKK", timePeriods=NULL,
                   aggregate=c("Province","District"), 
                   minAggregateCount=1, 
                   markerSize=c(10,40), 
                   colourBy="Province", 
                   showNames=TRUE,
                   ...)
r 复制代码
mapDrugResistancePrevalence (ctx, sampleSet="EBKK", timePeriods=NULL,
                   drugs="ALL", aggregate=c("Province","District"),
                   minAggregateCount=10, showNames=TRUE, markerSize=16,
                   ...)

参考

相关推荐
大数据CLUB4 小时前
基于spark的奥运会奖牌变化数据分析
大数据·hadoop·数据分析·spark
datagear5 小时前
如何在DataGear 5.4.1 中快速制作HTTP数据源服务端分页的数据表格看板
javascript·数据可视化
Chef_Chen8 小时前
从0开始学习R语言--Day39--Spearman 秩相关
开发语言·学习·r语言
好开心啊没烦恼9 小时前
Python 数据分析:计算,分组统计1,df.groupby()。听故事学知识点怎么这么容易?
开发语言·python·数据挖掘·数据分析·pandas
wenzhangli713 小时前
OneCode 图表组件核心优势解析
数据可视化
用户Taobaoapi20141 天前
母婴用品社媒种草效果量化:淘宝详情API+私域转化追踪案例
大数据·数据挖掘·数据分析
用户Taobaoapi20141 天前
Taobao agent USA丨美国淘宝代购1688代采集运系统搭建指南
数据挖掘·php
key061 天前
电子水母函数解析
数据分析
Brduino脑机接口技术答疑1 天前
脑机新手指南(二十一)基于 Brainstorm 的 MEG/EEG 数据分析(上篇)
数据挖掘·数据分析
镜舟科技1 天前
StarRocks × Tableau 连接器完整使用指南 | 高效数据分析从连接开始
starrocks·数据分析·数据可视化·tableau·连接器·交互式分析·mpp 数据库