需要R包版本2.3.1及以上
“小洁忘了怎么分身”创立的tinyarray 此代码复制粘贴即可运行
rm(list = ls())
#打破下载时间的限制,改前60秒,改后10w秒
options(timeout = 100000)
options(scipen = 20)#不要以科学计数法表示
library(tinyarray)
packageVersion("tinyarray")
#> [1] '2.3.2'
library(stringr)
geo = geo_download("GSE7305")
exp = geo$exp
exp = log2(exp+1)
boxplot(exp,las = 2)
pd = geo$pd
gpl_number = geo$gpl
# 分组信息
k = str_detect(pd$title,"Normal");table(k)
#> k
#> FALSE TRUE
#> 10 10
Group = ifelse(k,"Normal","Disease")
Group = factor(Group,levels = c("Normal","Disease"))
# 探针注释
find_anno(geo$gpl)
library(hgu133plus2.db);ids <- toTable(hgu133plus2SYMBOL)
head(ids)
#> probe_id symbol
#> 1 1007_s_at DDR1
#> 2 1053_at RFC2
#> 3 117_at HSPA6
#> 4 121_at PAX8
#> 5 1255_g_at GUCA1A
#> 6 1294_at UBA7
#差异分析和它的可视化
dcp = get_deg_all(exp,Group,ids,entriz = F)
table(dcp$deg$change)
#>
#> down stable up
#> 579 19621 624
head(dcp$deg)
#> logFC AveExpr t P.Value
#> 1 6.270309 8.436140 45.39552 0.000000000000000000000009106509
#> 2 3.943359 7.351799 35.25755 0.000000000000000000002600407155
#> 3 2.318498 6.631187 32.33367 0.000000000000000000017855505829
#> 4 4.905540 8.140399 30.78154 0.000000000000000000053206731115
#> 5 4.878195 6.815838 29.02740 0.000000000000000000195062651758
#> 6 4.106051 9.045949 28.82714 0.000000000000000000227319306208
#> adj.P.Val B probe_id symbol change
#> 1 0.0000000000000000002489492 41.58809 202992_at C7 up
#> 2 0.0000000000000000473924204 37.34483 204971_at CSTA up
#> 3 0.0000000000000001952499562 35.77275 228564_at LINC01116 up
#> 4 0.0000000000000004155825748 34.85700 208131_s_at PTGIS up
#> 5 0.0000000000000013331313106 33.74579 210002_at GATA6 up
#> 6 0.0000000000000013809647852 33.61341 212190_at SERPINE2 up
dcp$plots
library(ggplot2)
ggsave("deg.png",width = 15,height = 5)
#富集分析
deg = get_deg(exp,Group,ids)
genes = deg$ENTREZID[deg$change!="stable"]
head(genes)
#> [1] "730" "1475" "375295" "5740" "2627" "5270"
#有可能因为网络问题报错
g = quick_enrich(genes,destdir = tempdir())
names(g)
#> [1] "kk" "go" "kk.dot" "go.dot"
g[[1]][1:4,1:4]
#> category
#> hsa04610 Organismal Systems
#> hsa04514 Environmental Information Processing
#> hsa05150 Human Diseases
#> hsa04110 Cellular Processes
#> subcategory ID
#> hsa04610 Immune system hsa04610
#> hsa04514 Signaling molecules and interaction hsa04514
#> hsa05150 Infectious disease: bacterial hsa05150
#> hsa04110 Cell growth and death hsa04110
#> Description
#> hsa04610 Complement and coagulation cascades
#> hsa04514 Cell adhesion molecules
#> hsa05150 Staphylococcus aureus infection
#> hsa04110 Cell cycle
library(patchwork)
g[[3]]+g[[4]]
ggsave("enrich.png",width = 12,height = 7)
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原创声明:本文系作者授权腾讯云开发者社区发表,未经许可,不得转载。
如有侵权,请联系 cloudcommunity@tencent.com 删除。
原创声明:本文系作者授权腾讯云开发者社区发表,未经许可,不得转载。
如有侵权,请联系 cloudcommunity@tencent.com 删除。