[R] A question related to extracting peptides from indels for mouse

[Li, Aiguo (NIH/NCI) [E] via R-help]

Dear all,

I need to extract peptides from a long list of indels of mouse for neoantigen 
analysis.  Does anyone know a tool that will do it?

Thanks,

Anna

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Re: [R] [EXTERNAL] Re: A question of data frame filter based on another one

[Li, Aiguo (NIH/NCI) [E] via R-help]

Hi Eric,

Thanks for your quick response.  It works.

Have a nice weekend!

Aiguo

From: Eric Berger 
Date: Friday, February 18, 2022 at 3:35 PM
To: "Li, Aiguo (NIH/NCI) [E]" 
Cc: "r-help@r-project.org" 
Subject: [EXTERNAL] Re: [R] A question of data frame filter based on another one

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x[apply(y,MAR=1,sum) > 0,]


On Fri, Feb 18, 2022 at 10:24 PM Li, Aiguo (NIH/NCI) [E] via R-help 
mailto:r-help@r-project.org>> wrote:
I have tow dataframes as below:
> x
  id  g
1  1 21
2  3 52
3  2 43
4  4 94
5  5 35

> y
  id g
1  1 1
2  0 0
3  0 1
4  1 0
5  1 0

Results dataframe I want is:
1 21
2 43
4 94
5 35

Basically I want to extract all the values in x which corresponding those 
values =1 in y.

I tried:
x[which(y==1),].  It gets:
id  g
1 1 21
4 4 94
5 5 35
NA   NA NA
NA.1 NA NA

But missing the row: 2 43.

Any help will be appreciated.

Thanks,
Aiguo

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[R] A general question about targeted sequencing data analysis

[Li, Aiguo (NIH/NCI) [E] via R-help]

Dear all,

One of our PIs has a targeted sequencing dataset generated a while ago.  He is 
interested in finding out VAF of a group of genes.  This is the first dataset 
of this types we have.  I would be appreciative for any suggestions on 
pipelines for analyzing this type of data.

Thanks

Anna

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