具有特定值R的列 [英] Column with specific value R

问题描述

我有一个3列(基因，variant_type和样本)和两个列(途径和基因)中的另一列的数据框.在第二篇文章中，我列出了每种途径的基因.因此，现在我想创建一个由4列(基因，variant_type，样本和途径)组成的新数据框，以显示每个基因所存在的途径.有谁可以帮助我吗?预先感谢.

I have a data frame of 3 columns (genes, varian_type and samples) and another one of two columns (pathways and genes). In the second one I have a list of genes in each pathway. So now I would like to create a new data frame of 4 columns (genes, variant_type, samples and pathways) that shows the pathway or pathways in which each gene is present. Is there anyone who can help me? Thanks in advance.

1)

     Hugo_Symbol    Variant_Type         Tumor_Sample_Barcode
1       ZAP70          SNP           TCGA-E9-A1RC-01A-11D-A159-09

2)

structure(list(circuit_names = c("hsa04014__44", "hsa04014__33", 
"hsa04014__37", "hsa04014__24", "hsa04014__26", "hsa04014__30"
), mutated = c("ZAP70,NF1,MAPK1,RAF1,CSF1R,RASGRP1,MAP2K1,MAP2K1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,NF1,PLCG1,PLCG1,PLCG1", 
"ZAP70,NF1,AKT3,CSF1R,BAD,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,PIK3R5,NF1,BCL2L1,PLCG1,PLCG1,PLCG1,AKT3", 
"ZAP70,NF1,AKT3,CSF1R,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,PIK3R5,NF1,PLCG1,PLCG1,PLCG1,FOXO4,AKT3", 
"ZAP70,NF1,CSF1R,RGL2,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,NF1,PLCG1,PLCG1,PLCG1", 
"ZAP70,NF1,CSF1R,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,NF1,PLCG1,PLCG1,PLCG1,PLCE1", 
"ZAP70,NF1,CSF1R,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,NF1,PLCG1,PLCG1,PLCG1,PLCE1"
)), row.names = c(NA, 6L), class = "data.frame")

3)我不会这样子

    structure(list(Hugo_Symbol = c("ZAP70", "TTN", "TTN", "PRKCD", 
"PIK3CA", "TLR3"), Variant_Type = c("SNP", "SNP", "SNP", "SNP", 
"SNP", "SNP"), Tumor_Sample_Barcode = c("TCGA-E9-A1RC-01A-11D-A159-09", 
"TCGA-E9-A1RC-01A-11D-A159-09", "TCGA-E9-A1RC-01A-11D-A159-09", 
"TCGA-E9-A1RC-01A-11D-A159-09", "TCGA-E9-A1RC-01A-11D-A159-09", 
"TCGA-E9-A1RC-01A-11D-A159-09"), Pathways = c("hsa04014__44, hsa04014__33, hsa04014__37, hsa04014__24", 
"hsa04530__11 20 16", "hsa04530__11 20 16", "hsa04722__37, hsa04722__35, hsa04722__33", 
"hsa04151__25, hsa04151__37, hsa04151__73", "hsa04620__23")), row.names = c("6", 
"8", "9", "11", "13", "16"), class = "data.frame")

推荐答案

更新-更改了解决方法，以便它也可以处理OP指出的情况.即，如果Hugo_Symbol为NF1，则逻辑不应与NF11或NF12

Update - Changed solution approach so that it also handles the case pointed out by OP. i.e. if Hugo_Symbol is NF1 then logic should not matches NF11 or NF12

library(dplyr)
library(tidyr)

df1  %>%
  mutate(Hugo_Symbol = as.character(Hugo_Symbol)) %>%   #convert factor to character variable
  left_join(df2 %>%
              separate_rows(mutated, sep = ','), 
            by = c("Hugo_Symbol" = "mutated")) %>%
  group_by(Hugo_Symbol, Variant_Type, Tumor_Sample_Barcode) %>%
  summarise(Pathways = paste(unique(circuit_names), collapse = ","))   #combine distinct values in Pathways

给出

  Hugo_Symbol Variant_Type Tumor_Sample_Barcode         Pathways                                     
1 NF1         SNP          TCGA-E9-A1RC-01A-11D-A159-09 hsa04014__44,hsa04014__33

样本数据:

df1 <- structure(list(Hugo_Symbol = "NF1", Variant_Type = "SNP", Tumor_Sample_Barcode = "TCGA-E9-A1RC-01A-11D-A159-09"), .Names = c("Hugo_Symbol", 
"Variant_Type", "Tumor_Sample_Barcode"), class = "data.frame", row.names = "1")

df2 <- structure(list(circuit_names = c("hsa04014__44", "hsa04014__33", 
"hsa04014__37", "hsa04014__24"), mutated = c("ZAP70,NF1,MAPK1,RAF1,CSF1R,RASGRP1,MAP2K1", 
"ZAP70,NF1,AKT3,CSF1R,BAD,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1", 
"ZAP70,NF11,AKT3,CSF1R,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1,RASGRF", 
"ZAP70,NF12,CSF1R,RGL2,RASGRP1,RASGRF1,RASGRF1,RASGRF1,RASGRF1"
)), .Names = c("circuit_names", "mutated"), class = "data.frame", row.names = c("1", 
"2", "3", "4"))

这篇关于具有特定值R的列的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！