about reshaping a data frame
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Bogdan ▴ 620
@bogdan-2367
Last seen 1 hour ago
Palo Alto, CA, USA

Dear all,

although it is a more general R question, if you do not mind having me asking the question on BioC list, as it relates to the packages maftools and ComplexHeatmap.  

I would appreciate please a piece of help regarding the use of acast/dcast functions in reshape2 package (the output matrix will serve as input into maftools and ComplexHeatmap). 

Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below):

Sample    Gene  Type
22M       AEBP1   SNV
17M       AEBP1   SNV
22M         ATR   INDEL
22M         ATR   SNV
11M         BTK   SNV
11M         BTK INDEL

I would like to transform this DATAFRAME into a MATRIX that has :

-- GENE on ROWS,

-- SAMPLE on COLUMNS,

-- and the elements of the matrix are SNV or INDEL (ie the types of mutations). 

The R code starts with :

y <- data.frame(Sample = x$Sample, Gene = x$Gene, Type=x$Type) 

z <- acast(y, Cancer_Gene ~ Sample)

although in z, I do not have the information on Type (i.e.SNV or INDEL).

thanks a lot, 

-- bogdan

maftools complexheatmap • 703 views
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Haiying.Kong ▴ 110
@haiyingkong-9254
Last seen 2.5 years ago
Germany

Because there are redundancies:

22M         ATR   INDEL
22M         ATR   SNV

  and
11M         BTK   SNV
11M         BTK INDEL

you cannot do reshaping on the original data.

 you need to collapse the data to something like:

Sample    Gene  Type
22M       AEBP1   SNV
17M       AEBP1   SNV
22M         ATR   INDEL,SNV
11M         BTK   SNV,INDEL

  This can be done with:
b = aggregate(y[ ,-(1:2)], by=list(y$Sample, y$Gene), FUN=paste)

names(b) = names(Y)

Then, you can do reshaping with:

wide = reshape(b, idvar="Gene", timevar="Sample", direction="wide")

  You can get more information from :

https://stats.idre.ucla.edu/r/faq/how-can-i-reshape-my-data-in-r/

 

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Dear Haiying, thank you very much for suggestions and kind help ;)

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