Rscript match

Question

[priyanka]

I have two dataframe.

One is vcf. Its content is : **

head(vcf)
  X.CHROM       POS           ID      CHROM_POS
1    chr1 100000421 rs1047982323 chr1_100000421
2    chr1 100000827 rs1375386196 chr1_100000827
3    chr1 100001753  rs866745787 chr1_100001753
4    chr1 100001904 rs1416462966 chr1_100001904
5    chr1 100002334 rs1220478954 chr1_100002334
6    chr1 100002490  rs181634796 chr1_100002490**

and the other is mashr. Its content is:

head(mashr)
           RSID1         RSID2_
1 chr1_169894240 chr1_169894240
2 chr1_169894240 chr1_169891332
3 chr1_169891332 chr1_169891332
4 chr1_169661963 chr1_169661963
5 chr1_169661963 chr1_169697456
6 chr1_169697456 chr1_169697456

I want to count the number of matches between these two dataframe in terms of chr_pos. and number of chr_pos in vcf dataframe missed in mash. I wrote this command:

which(vcf$CHROM_POS == mashr$RSID1)

but its showing error: the error:

integer(0)
Warning message:
In vcf$CHROM_POS == mashr$RSID1 :
  longer object length is not a multiple of shorter object length

I know that this error is related to the fact that the length is varying.

Can anyone tell me how to do this.

I want to find the number of similar chrom_pos between the two dataframe and chrom_pos missed between the two dataframe

[Ram]

Use merge or dplyr's join functions. Google should get you started on basic tutorials for these.

Answer 1

[bioinformatics2020]

There are many ways to go about this. Here's something I wrote up quick and dirty. I separated out mashr into two new data-frames based upon their columns.

#install.packages("tidyverse")    
library(tidyverse)

mashr_one <- tibble(CHROM_POS = mashr$RSID1,
                        Group = "RSID1")

mashr_two <- tibble(CHROM_POS = mashr$RSID2_,
                        Group = "RSID2")

result <- full_join(vcf, mashr_one)
result2 <- full_join(vcf, mashr_two)
bind_rows(result, result2)

[priyanka]

Hey, Thank you so much. This worked for me.