Users' documentation for Genetranassoc in c++

Installation

Compiled version:

Compiled version for linux.-After you have succesfully obtained the archive you can execute the following Unix commands to install the program:

• gunzip [filename].gz
• chmod 755 [filename]

Source code version:

Source code version for linux.-After you have succesfully obtained the archive you can execute the following Unix commands to install the program:

• tar xvzf Genetranassoc2.0.tar.gz
• cd Genetranassoc2.0
• make

Execution

To use Genetranassoc, write the following command line:

./Genetranassoc2 <filename1> <filename2> <filename3> <output filename> <number of heading fileds (default: 1)> <number of permutations to be used (0: no permutation test, default)> <whether genotypes are in extended makeped format with individual ID read from column 7 -.gou files- (1); in makeped format -PLINK- with individual ID read from the second column (0) or in vcf format with only one column for phenotype -first column, individual ID- (2). Default is 0 (makedped format)

where <filename1> is the input file with gene expression profiles whose format is shown below

<filename2> is the input file with SNP genotypes in makeped (PLINK), extended makeped format (as shown below) or cvf format and

<filename3> is the input file with SNP genotypes that must be in makeped, extended makeped or vcf format as well (the same format used for the input file filename2) and which will be used as a reference file to choose the major alleles. In the case this is not important, filename2 must be provided again and major alleles will be those considering this file.

Note: The program name Genetranassoc may be different depending on the version you have installed. As an example, if you used the compiled version for linux x32 the name is Genetranassoc1.0_x32.

Note 2: In the cas of using extended makeped, there must be two one-column text files with physical positions and rs numbers with same name as filename2 and filename3 but extensions .pou and .rs respectively. In the case of using makeped format (PLINK) a .map file with the same name is required.

Format of the input file with gene expression profiles

A csv text file of gene expression values with a heading row and n more rows, one for each expression data variable.

The number of columns is h+m, with h being the number of heading columns and m being the number of individuals.

Here there is an example of a gene expression file with 2 heading columns.

Extnded mkeped format of the input genotype file

A text file of SNP data set, in post-makeped format as described here:

One row per individual, 7 + 2xTotalSNPs columns, with TotalSNPs being the number of SNPs. Columns must be separared by a blank or tab character.Each column must contain an integer. See an example of input file.

Description of columns:

• Column 1: family code
• Column 2: individual code
• Column 3: father code (0 if the individual is not a child)
• Column 4: mother code (0 if the individual is not a child)
• Column 5: gender
• Column 6: affection status
• Column 7: another individual id
• Columns 8 until 7+2*TotalSNPs: SNPs values (each SNP uses two contiguous columns). Example: if SNP1 value for an individual is 12 (heterozygous), column8 will have the value 1 and column9 will have the 2.

Format of the input file with physical positions

One position per row. Click here to see an example.

Format of the input file with rs numbers

One position per row. Click here to see an example.

Output for the program Genetranassoc

The output will be written at a file which is a csv text file with a heading and one row for each pair of SNP-expression data variable (first and second column), the Spearman correlation value (third column), raw p value (fourth column), -log10 of the raw p value (fifth column) and, in the case permutation tests were selected, permutation p values (sixth column) and -log10 of the permutation p values (seventh column).