听说你想找TCGA的乳腺癌亚型

rm(list = ls())
a = read.delim("TCGASubtype.20170308.tsv.gz")
head(a)

##          sampleID                         Subtype_mRNA
## 1 TCGA-OR-A5J1-01 steroid-phenotype-high+proliferation
## 2 TCGA-OR-A5J2-01 steroid-phenotype-high+proliferation
## 3 TCGA-OR-A5J3-01               steroid-phenotype-high
## 4 TCGA-OR-A5J4-01                                 <NA>
## 5 TCGA-OR-A5J5-01               steroid-phenotype-high
## 6 TCGA-OR-A5J6-01               steroid-phenotype-low 
##     Subtype_DNAmeth Subtype_protein Subtype_miRNA Subtype_CNA
## 1         CIMP-high            <NA>       miRNA_1       Quiet
## 2          CIMP-low               1       miRNA_1       Noisy
## 3 CIMP-intermediate               3       miRNA_6 Chromosomal
## 4         CIMP-high            <NA>       miRNA_6 Chromosomal
## 5 CIMP-intermediate            <NA>       miRNA_2 Chromosomal
## 6          CIMP-low               2       miRNA_1       Noisy
##   Subtype_Integrative Subtype_other      Subtype_Selected
## 1                COC3           C1A         ACC.CIMP-high
## 2                COC3           C1A          ACC.CIMP-low
## 3                COC2           C1A ACC.CIMP-intermediate
## 4                <NA>          <NA>         ACC.CIMP-high
## 5                COC2           C1A ACC.CIMP-intermediate
## 6                COC1           C1B          ACC.CIMP-low

library(stringr)
k = str_starts(a$Subtype_Selected,"BRCA");table(k)

## k
## FALSE  TRUE 
##  6516  1218

a = a[k,]
table(a$Subtype_mRNA)

## 
##  Basal   Her2   LumA   LumB Normal 
##    193     82    581    219    143

# 表达矩阵
load("brca_exp.Rdata")
brca[1:4,1:4]

##                    TCGA-E2-A1L7-11A-33R-A144-07
## ENSG00000000003.15                         4209
## ENSG00000000005.6                            71
## ENSG00000000419.13                         1611
## ENSG00000000457.14                         1217
##                    TCGA-E2-A1L7-01A-11R-A144-07
## ENSG00000000003.15                         1689
## ENSG00000000005.6                            16
## ENSG00000000419.13                         1810
## ENSG00000000457.14                         1098
##                    TCGA-AR-A0U0-01A-11R-A109-07
## ENSG00000000003.15                         1590
## ENSG00000000005.6                             0
## ENSG00000000419.13                         2073
## ENSG00000000457.14                          889
##                    TCGA-BH-A28O-01A-11R-A22K-07
## ENSG00000000003.15                         4583
## ENSG00000000005.6                           135
## ENSG00000000419.13                         1531
## ENSG00000000457.14                         1445

head(colnames(brca))

## [1] "TCGA-E2-A1L7-11A-33R-A144-07"
## [2] "TCGA-E2-A1L7-01A-11R-A144-07"
## [3] "TCGA-AR-A0U0-01A-11R-A109-07"
## [4] "TCGA-BH-A28O-01A-11R-A22K-07"
## [5] "TCGA-A2-A0D4-01A-11R-A00Z-07"
## [6] "TCGA-E9-A1R4-01A-21R-A14D-07"

# 缩短id
colnames(brca) = str_sub(colnames(brca),1,15)
rownames(a) = NULL
a = tibble::column_to_rownames(a,"sampleID")
# 匹配两个表格的顺序
s = intersect(colnames(brca),rownames(a))
exp = brca[,s]
a = a[s,]
# 提取
k1 = a$Subtype_mRNA %in% c("LumA","LumB");table(k1)

## k1
## FALSE  TRUE 
##   415   800

a = a[k1,]
exp = exp[,k1]
exp[1:4,1:4]

##                    TCGA-E2-A1L7-01 TCGA-A2-A0D4-01
## ENSG00000000003.15            1689            1550
## ENSG00000000005.6               16              45
## ENSG00000000419.13            1810            2710
## ENSG00000000457.14            1098            2026
##                    TCGA-E9-A1R4-01 TCGA-AO-A1KQ-01
## ENSG00000000003.15             711             825
## ENSG00000000005.6               15               3
## ENSG00000000419.13            1943            2626
## ENSG00000000457.14            1285            1058