Question

Identifying Genes in Gene_table1 that are also present in Gene_table2 and produce a new Gene_tabel with information from Gene_table2

0

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3.5 years ago

Ksandersen ▴ 20

Hello All

I have two gene tables in R. I want to make some code, which can do the following.

Take the genes in Gene_Tabel1 and compare if they are present in Gene_tabel2
If The genes are present in Gene_Tabel2 I want to add the information from Gene_Table2 into a new Table as shown in Gene_Table3

I believe this could be done through a loop and some extra coding. However, I do not know exactly to produce this code (I am very new to coding).

Gene_Tabel1:

     Gene
1   ENSDARG00000063908
2   ENSDARG00000070083
3   ENSDARG00000063911
4   ENSDARG00000099499
5   ENSDARG00000092553
6   ENSDARG00000056008
7   ENSDARG00000098355
8   ENSDARG00000088383
9   ENSDARG00000063924
10   ENSDARG00000068738

etc...

Gene_Tabel2:

     Gene
1   ENSDARG00000102123   phtf2
2   ENSDARG00000114503   phtf21
3   ENSDARG00000070083   atp5f1b
4   ENSDARG00000098311   si:zfos-932h1.3
5   ENSDARG00000104839   mansc1
6   ENSDARG00000100143   Irp6
7   ENSDARG00000068738   dusp16
8   ENSDARG00000104049   crebl2
9   ENSDARG00000102226   gpr19
10  ENSDARG00000103095   tbk1

etc...

Gene_Tabel3:

    Gene
1: ENSDARG00000070083   atp5f1b
2: ENSDARG00000068738   dusp16

I hope there is someone who can give me a helping hand.

Best Regards
Kristian Andersen

RNA-Seq R • 951 views

ADD COMMENT • link updated 3.3 years ago by Biostar 20 • written 3.5 years ago by Ksandersen ▴ 20

2

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You should look into the merge function. That does exactly what you're looking for.

ADD REPLY • link 3.5 years ago by Ram 43k

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Thanks for the hint. :) I figured out how to do the merging.

I used the following code:

merge(Gene_Table1, Gene_Table2, by = "Gene", sort = FALSE)

ADD REPLY • link updated 3.5 years ago by Ram 43k • written 3.5 years ago by Ksandersen ▴ 20

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Could you posible provide me with the coding? It doesn't seem to work for me?

ADD REPLY • link 3.5 years ago by Ksandersen ▴ 20

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Please read up on the documentation and show us what you've tried. Asking for exact code is not good etiquette.

ADD REPLY • link 3.5 years ago by Ram 43k

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Would linux commands work for you? AWK and grep?

ADD REPLY • link 3.5 years ago by Fatima ▴ 1000

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Please do not supply users with code - it interferes with their learning.

ADD REPLY • link 3.5 years ago by Ram 43k

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Can you post some example data from both tables using dput(head(Gene_Table1)) and dput(head(Gene_Table2))?

ADD REPLY • link 3.5 years ago by rpolicastro 13k