Mapping common identifiers between two files
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4.3 years ago

Hi,

I have two different *.csv files with different number of rows and columns. Based the the merge function I was able to combine both the files based on mapping on the ProbeID column (common between both the files) and save all the data in a output file. However, I notice that even the unmapped rows are getting saved in the output file. I am only interested in the mapped IDs common between the two files. Please assist me with this.

File_1 has 33298 ProbeIDs
File_2 has 41270 ProbeIDs
Combined file has 41270 ProbeIDs

Combined<- merge(File_1, File_2, by="ProbeID")

Thank you,

Toufiq

merge mapping csv R • 1.1k views
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Have a look into dplyr joins. dplyr::left_join(df1, df2) keep all the rows from df1. dplyr::right_join(df1, df2) keep all the rows from df2.

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Provide reproducible example input and expected output. Your code looks fine and should only return matching rows that have common "ProbeID"s in both files, test this example:

merge(data.frame(x = 1:3, y = 11),
      data.frame(x = 2:4, z = 22), by = "x")
#   x  y  z
# 1 2 11 22
# 2 3 11 22

See this StackOverflow post for more examples and other merging options:

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