Example of a LowMACA object

Description

A data frame containing TCGA AML data in the format accepted by LowMACA

Usage

data("LowMACA_AML")

Format

A data.frame of 8 columns:

1. Entrez gene ID number

2. Gene_Symbol HGNC official gene symbol

3. Amino_Acid_Letter original amino acid letter in the position of the mutation

4. Amino_Acid_Position position of the mutation relative to the protein

5. Amino_Acid_Change amino acid change in hgvs format, like G12V

6. Mutation_Type classification of mutation according to MAF format.

7. Sample name of the sample where the mutation was found

8. Tumor_Type type of tumor, if applicable

Source

Adapted from TCGA ftp repository

See Also

MAF format specification HGVS

Examples

#Load LowMACA_AML and show its structure
data(LowMACA_AML)
str(LowMACA_AML)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LowMACA)
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .).
BEGIN failed--compilation aborted.
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: running command '/usr/bin/perl -MXML::Simple -e 1' had status 2 
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LowMACA/LowMACA_AML.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LowMACA_AML
> ### Title: Example of a LowMACA object
> ### Aliases: LowMACA_AML
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #Load LowMACA_AML and show its structure
> data(LowMACA_AML)
> str(LowMACA_AML)
'data.frame':	2319 obs. of  8 variables:
 $ Entrez             : int  4519 6913 126637 1788 3417 2917 91074 121391 5781 57634 ...
 $ Gene_Symbol        : chr  "MT-CYB" "TBX15" "TCHHL1" "DNMT3A" ...
 $ Amino_Acid_Letter  : chr  "I" "I" "Q" "R" ...
 $ Amino_Acid_Position: num  7 59 879 882 132 474 649 305 61 596 ...
 $ Amino_Acid_Change  : chr  "I7T" "I59F" "Q879R" "R882C" ...
 $ Mutation_Type      : chr  "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" ...
 $ Sample             : chr  "TCGA-AB-2802" "TCGA-AB-2802" "TCGA-AB-2802" "TCGA-AB-2802" ...
 $ Tumor_Type         : chr  "aml" "aml" "aml" "aml" ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>