CODEWITHSUNDEEP
r
user324810
user324810

Reputation: 606

R: How to check if each element of my list partially match a column in dataframe?

I have a test_list

test_list <- list("hg38:Chr12:8823762", "hg38:Chr10:50814012", "hg19:Chr12:8990070", 
        "hg38:chr1:16949", "hg38:chr9:342484")

and I want to check if each element in my list partially match my column Extra_information in df

df <- structure(list(Extra_information = c("hg38:Chr10:50814012, hg19:Chr10:52573772, CpG:Mutation may have occured by deamination of methylated CpG dinucleotide", 
"hg38:Chr12:8822661, hg19:Chr12:8975257, COM:Patient is homozygous for c.706C>G p.Leu236Val in SLC26A4., dbSNP:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409944554", 
"hg38:Chr12:8823729, hg19:Chr12:8976325, COM:Variant of unknown significance. Clinical features descr. in supplementary table 2. functional study., dbSNP:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766201825", 
"hg38:Chr12:8823762, hg19:Chr12:8976358, COM:VUS Table 2. RIT1 variant also present.", 
"hg38:Chr12:8835642, hg19:Chr12:8988238, COM:VUS Table 2. SOS1 and CBL variants also present., dbSNP:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs11047499", 
"hg38:Chr12:8837474, hg19:Chr12:8990070, dbSNP:http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs863224952"
)), row.names = c(NA, 6L), class = "data.frame")

to obtain a dataframe of my list with the values 1 for TRUE and 0 for FALSE:

test_df <- structure(list(Entries = c("hg38:Chr12:8823762", "hg38:Chr10:50814012", "hg19:Chr12:8990070", 
        "hg38:chr1:16949", "hg38:chr9:342484"), Values = c(1,1,1,0,0)), row.names = c(NA, 5L), class = "data.frame"))

output

How can I achieve the desired output ?

Thanks in advance.

Upvotes: 0

Views: 45

Answers (2)

Ian Campbell
Ian Campbell

Reputation: 24790

Here's a base R approach. 

data.frame(Entries = unlist(test_list),
           Values = sapply(test_list,function(x){
             as.numeric(length(grep(x,df$Extra_information)) > 0)
             }))
#              Entries Values
#1  hg38:Chr12:8823762      1
#2 hg38:Chr10:50814012      1
#3  hg19:Chr12:8990070      1
#4     hg38:chr1:16949      0
#5    hg38:chr9:342484      0

Upvotes: 2

akrun
akrun

Reputation: 887078

We could use agrepl to check for partial matches between the 'test_list' elements and the 'Extra_information' (from base R only)

Values <- +(sapply(test_list, function(x) any(agrepl(x, df$Extra_information))))
data.frame(Entries = unlist(test_list), Values)
#              Entries Values
#1  hg38:Chr12:8823762      1
#2 hg38:Chr10:50814012      1
#3  hg19:Chr12:8990070      1
#4     hg38:chr1:16949      0
#5    hg38:chr9:342484      0

Upvotes: 1

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