R中的部分合并数据集

Question

I have two data files that look like this:

bin chrom   chromStart  chromEnd    name    score   strand
23  chr1    119537649   119537708   A_14_P109202    1000    +
109 chr1    37879762    37879821    A_16_P15088121  1000    +
129 chr1    59113425    59113484    A_16_P00074945  1000    +
138 chr1    68288459    68288517    A_16_P00088142  1000    +

and

Hybridization REF   TCGA-02-0001-01C-01D-0185-02       
Composite Element REF   normalizedLog2Ratio    
A_14_P112718    0.034472223    
A_16_P15000916  -0.038733669       
A_16_P15001074  -0.498562753       
A_16_P00000012  -0.269915751     

.

Using the names from the first column of the second file, I need to extract additional data from the data table in the first file. However, not every name in the second file appears in the first. I am having problems getting the files to merge properly. Any help is much appreciated.

Answer 1

if you place all.x=TRUE in the merge command; all of the records from the first data frame will be in the merged dataframe, even if they don't have a match in the second. Is that the problem you were encountering? In the example that you gave none of the rownames matched any of the observations in the name variable.

bin<-c(23,109,129,138)
chrom<-c("chr1","chr1","chr1","chr1")
chromStart<-c(119537649,37879762,59113425,68288459)  
name<-c("A_14_P109202", "A_16_P15088121", "A_16_P00074945","A_16_P00088142")
b<- data.frame(cbind(bin,chrom,chromStart,name))

y <- data.frame(c(0.034472223    ,-0.038733669 , -0.498562753 ,-0.269915751)) 
rownames(y)<-c("A_14_P112718","A_16_P15000916","A_16_P15001074","A_16_P00000012")


print(b)
print(y)

#check the rows
nrow(b)
nrow(y)

#write rownames to new variable
y$name <- rownames(y)

#conduct merge
newdataframe <- merge(b, y, by=("name"), all.x = TRUE )

#check number of rows
nrow(newdataframe)