博客园 - 月光边境Eric
uuid:24b78886-0ed1-41c2-8670-e3f31dcf42c4;id=20213
2021-04-01T00:29:20Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
feed.cnblogs.com
https://www.cnblogs.com/SWTwanzhu/p/14458789.html
安装conda,并添加频道及配置环境 - 月光边境Eric
安装conda wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh ##-c 表示断点续传 bash Miniconda3-latest-Linux-x86_64.sh 添加频道 conda co
2021-02-28T13:42:00Z
2021-02-28T13:42:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】安装conda wget -c https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh ##-c 表示断点续传 bash Miniconda3-latest-Linux-x86_64.sh 添加频道 conda co <a href="https://www.cnblogs.com/SWTwanzhu/p/14458789.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/14336762.html
根据数据库中已有的变量创建新的变量并整合到原始数据框中-三种方式 - 月光边境Eric
第一种 > mydata <- data.frame(x1 = c(2,2,6,4),x2 = c(3,4,2,8)) > mydata x1 x2 1 2 3 2 2 4 3 6 2 4 4 8 > mydata$sumx <- mydata$x1 + mydata$x2 > mydata x1
2021-01-27T12:21:00Z
2021-01-27T12:21:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】第一种 > mydata <- data.frame(x1 = c(2,2,6,4),x2 = c(3,4,2,8)) > mydata x1 x2 1 2 3 2 2 4 3 6 2 4 4 8 > mydata$sumx <- mydata$x1 + mydata$x2 > mydata x1 <a href="https://www.cnblogs.com/SWTwanzhu/p/14336762.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/14330683.html
R-根据ID提取行信息 - 月光边境Eric
创建数据框,然后根据给定ID提取对应行的信息,特别是给定的ID比较多的时候,其实很简单! > patientID <- c("A","B","C","D") > age <- c(25,34,44,52) > DB <- c("T1","T2","T1","T1") > status <- c("P
2021-01-26T07:40:00Z
2021-01-26T07:40:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】创建数据框,然后根据给定ID提取对应行的信息,特别是给定的ID比较多的时候,其实很简单! > patientID <- c("A","B","C","D") > age <- c(25,34,44,52) > DB <- c("T1","T2","T1","T1") > status <- c("P <a href="https://www.cnblogs.com/SWTwanzhu/p/14330683.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13232830.html
逻辑值 - 月光边境Eric
用逻辑值访问数据框或者别的,是循环访问嘛?特别是遇到那种下标出界的。。。
2020-07-03T13:36:00Z
2020-07-03T13:36:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】用逻辑值访问数据框或者别的,是循环访问嘛?特别是遇到那种下标出界的。。。 <a href="https://www.cnblogs.com/SWTwanzhu/p/13232830.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13210866.html
step-1 - 月光边境Eric
gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) if(F){ gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) save(gset,fil
2020-06-29T14:42:00Z
2020-06-29T14:42:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) if(F){ gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) save(gset,fil <a href="https://www.cnblogs.com/SWTwanzhu/p/13210866.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13198399.html
视频第5讲-ID转换 - 月光边境Eric
查找芯片平台(比如GSE42872的平台文件GPL6244)对应的数据包: 参考:http://www.bio-info-trainee.com/1399.html gpl organism bioc_package 1 GPL32 Mus musculus mgu74a 2 GPL33 Mus m
2020-06-27T07:09:00Z
2020-06-27T07:09:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】查找芯片平台(比如GSE42872的平台文件GPL6244)对应的数据包: 参考:http://www.bio-info-trainee.com/1399.html gpl organism bioc_package 1 GPL32 Mus musculus mgu74a 2 GPL33 Mus m <a href="https://www.cnblogs.com/SWTwanzhu/p/13198399.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13176846.html
通过向量访问矩阵 - 月光边境Eric
a = matrix(1:20, nrow = 4,dimnames = list(c("第1行", "第2行", "第3行", "第4行"), c("第1列", "第2列", "第3列", "第4列", "第5列"))) a a[c(1, 3), c(2, 4)] a[c(1, 3),] a[,
2020-06-22T06:55:00Z
2020-06-22T06:55:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】a = matrix(1:20, nrow = 4,dimnames = list(c("第1行", "第2行", "第3行", "第4行"), c("第1列", "第2列", "第3列", "第4列", "第5列"))) a a[c(1, 3), c(2, 4)] a[c(1, 3),] a[, <a href="https://www.cnblogs.com/SWTwanzhu/p/13176846.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13127313.html
跟着jmzeng学习GEO数据分析-GEO42872_1--题外 - 月光边境Eric
##这个可以跑if(T){ gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) save(gset,file ="GSE42872_eSet.Rdata") } ##也就说if(!file.exists(f))等同于if(
2020-06-14T14:05:00Z
2020-06-14T14:05:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】##这个可以跑if(T){ gset <- getGEO("GSE42872",destdir = ".",AnnotGPL = F,getGPL = F) save(gset,file ="GSE42872_eSet.Rdata") } ##也就说if(!file.exists(f))等同于if( <a href="https://www.cnblogs.com/SWTwanzhu/p/13127313.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13083999.html
step2-check.R - 月光边境Eric
load(file = 'step1-output.Rdata') table(group_list) # 每次都要检测数据 dat[1:4,1:4] ## 下面是画PCA的必须操作,需要看说明书。 dat=t(dat)#画PCA图时要求是行名时样本名,列名时探针名,因此此时需要转换 dat=as.
2020-06-10T03:33:00Z
2020-06-10T03:33:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】load(file = 'step1-output.Rdata') table(group_list) # 每次都要检测数据 dat[1:4,1:4] ## 下面是画PCA的必须操作,需要看说明书。 dat=t(dat)#画PCA图时要求是行名时样本名,列名时探针名,因此此时需要转换 dat=as. <a href="https://www.cnblogs.com/SWTwanzhu/p/13083999.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/13022162.html
跟着jmzeng学习GEO数据分析-GEO42872_1 - 月光边境Eric
f='GSE42872_eSet.Rdata' ##原文操作如此,是不是作者的习惯,先命名 # https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42872 library(GEOquery) # 这个包需要注意两个配置,一般来说自动化的配置
2020-05-31T14:45:00Z
2020-05-31T14:45:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】f='GSE42872_eSet.Rdata' ##原文操作如此,是不是作者的习惯,先命名 # https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42872 library(GEOquery) # 这个包需要注意两个配置,一般来说自动化的配置 <a href="https://www.cnblogs.com/SWTwanzhu/p/13022162.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12996313.html
%in%-ls()-rm(list = ls()) - 月光边境Eric
R中 %in% 的含义(from lzmcbody的回答): 每个元素都会被判断一次,返回逻辑值。 ls() 列出当前工作环境中所有变量--GEO数据step1用到的 > ls() [1] "a" "dat" "gpl" "group_list" "gset" "ids" [7] "pd" "pro
2020-05-30T23:35:00Z
2020-05-30T23:35:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】R中 %in% 的含义(from lzmcbody的回答): 每个元素都会被判断一次,返回逻辑值。 ls() 列出当前工作环境中所有变量--GEO数据step1用到的 > ls() [1] "a" "dat" "gpl" "group_list" "gset" "ids" [7] "pd" "pro <a href="https://www.cnblogs.com/SWTwanzhu/p/12996313.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12970194.html
getGEO()无法下载文件:InternetOpenUrl失败:’无法与服务器建立连接' - 月光边境Eric
其实加载GEOquery包的时候就出现options()的这行代码 > library(GEOquery) 载入需要的程辑包:Biobase 载入需要的程辑包:BiocGenerics 载入需要的程辑包:parallel 载入程辑包:‘BiocGenerics’ The following obje
2020-05-26T23:22:00Z
2020-05-26T23:22:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】其实加载GEOquery包的时候就出现options()的这行代码 > library(GEOquery) 载入需要的程辑包:Biobase 载入需要的程辑包:BiocGenerics 载入需要的程辑包:parallel 载入程辑包:‘BiocGenerics’ The following obje <a href="https://www.cnblogs.com/SWTwanzhu/p/12970194.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12967362.html
read.table()-1 - 月光边境Eric
所以打开读取GSE42872_series_matrix.txt.gz文件时,参数comment.char = "!"就表示!后面的注释文件不用读取。 > exprSet <- read.table("GSE42872_series_matrix.txt.gz",sep = "\t",fill =
2020-05-26T10:43:00Z
2020-05-26T10:43:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】所以打开读取GSE42872_series_matrix.txt.gz文件时,参数comment.char = "!"就表示!后面的注释文件不用读取。 > exprSet <- read.table("GSE42872_series_matrix.txt.gz",sep = "\t",fill = <a href="https://www.cnblogs.com/SWTwanzhu/p/12967362.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12966942.html
从Bioconductor安装包 - 月光边境Eric
以GEOquery为例 if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GEOquery")
2020-05-26T09:36:00Z
2020-05-26T09:36:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】以GEOquery为例 if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GEOquery") <a href="https://www.cnblogs.com/SWTwanzhu/p/12966942.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12954814.html
热图一 - 月光边境Eric
p <- ggplot(data_m, aes(x=variable,y=ID)) + xlab("samples") + theme_bw() + theme(panel.grid.major = element_blank()) + theme(legend.key=element_blank(
2020-05-25T00:59:00Z
2020-05-25T00:59:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】p <- ggplot(data_m, aes(x=variable,y=ID)) + xlab("samples") + theme_bw() + theme(panel.grid.major = element_blank()) + theme(legend.key=element_blank( <a href="https://www.cnblogs.com/SWTwanzhu/p/12954814.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12951166.html
R语言学习-绘制热图初步 - 月光边境Eric
> txt <- "ID;Zygote;2_cell;4_cell;8_cell + Gene_1;1;2;3;4 + Gene_2;6;5;4;5 + Gene_3;0.6;0.5;0.4;0.4" > txt [1] "ID;Zygote;2_cell;4_cell;8_cell\nGene_1
2020-05-24T07:36:00Z
2020-05-24T07:36:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】> txt <- "ID;Zygote;2_cell;4_cell;8_cell + Gene_1;1;2;3;4 + Gene_2;6;5;4;5 + Gene_3;0.6;0.5;0.4;0.4" > txt [1] "ID;Zygote;2_cell;4_cell;8_cell\nGene_1 <a href="https://www.cnblogs.com/SWTwanzhu/p/12951166.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12943784.html
访问数据框和矩阵的一点区别-拾遗 - 月光边境Eric
> data[1:3,] ##data[1:3,]与data[1:3]的不同,前者访问前三行,后者访问前三列,等同于data[,1:3] untrt_N61311 untrt_N052611 untrt_N080611 untrt_N061011 trt_N61311 FN1 245667.66 4
2020-05-23T10:17:00Z
2020-05-23T10:17:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】> data[1:3,] ##data[1:3,]与data[1:3]的不同,前者访问前三行,后者访问前三列,等同于data[,1:3] untrt_N61311 untrt_N052611 untrt_N080611 untrt_N061011 trt_N61311 FN1 245667.66 4 <a href="https://www.cnblogs.com/SWTwanzhu/p/12943784.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/12932858.html
PCA - 月光边境Eric
#加载R包 > library(psych)> library(reshape2)> library(ggplot2)> library(factoextra) ##提前把名为ehbio_salmon.DESeq2.normalized.symbol.txt的文件放在工作目录,以制表符分割的.txt
2020-05-21T11:34:00Z
2020-05-21T11:34:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】#加载R包 > library(psych)> library(reshape2)> library(ggplot2)> library(factoextra) ##提前把名为ehbio_salmon.DESeq2.normalized.symbol.txt的文件放在工作目录,以制表符分割的.txt <a href="https://www.cnblogs.com/SWTwanzhu/p/12932858.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/6137867.html
python教程--列表补遗一 - 月光边境Eric
>>> c = ['wonderful', 'yarn', 1, 2, 3] >>> c ['wonderful', 'yarn', 1, 2, 3] >>> d = [i * 2 for i in c] >>> d ['wonderfulwonderful', 'yarnyarn', 2, 4,
2016-12-06T07:48:00Z
2016-12-06T07:48:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】>>> c = ['wonderful', 'yarn', 1, 2, 3] >>> c ['wonderful', 'yarn', 1, 2, 3] >>> d = [i * 2 for i in c] >>> d ['wonderfulwonderful', 'yarnyarn', 2, 4, <a href="https://www.cnblogs.com/SWTwanzhu/p/6137867.html" target="_blank">阅读全文</a>
https://www.cnblogs.com/SWTwanzhu/p/6134353.html
python核心编程第六章练习--6.5.d - 月光边境Eric
字符串的一些方法: string.split(str) 以str 为分隔符(默认为空隔)切片string,如果num有指定值,则仅分隔num个子字符串. string.count(str) 计算str在string中出现的次数。 string.casefold() 将string所有的字符改为小写
2016-12-05T08:15:00Z
2016-12-05T08:15:00Z
月光边境Eric
https://www.cnblogs.com/SWTwanzhu/
【摘要】字符串的一些方法: string.split(str) 以str 为分隔符(默认为空隔)切片string,如果num有指定值,则仅分隔num个子字符串. string.count(str) 计算str在string中出现的次数。 string.casefold() 将string所有的字符改为小写 <a href="https://www.cnblogs.com/SWTwanzhu/p/6134353.html" target="_blank">阅读全文</a>