Generic

This section allows the user to download phenotypic and genotypic data about Samples in a generic format that is suitable to be imported by calculus or statistical packages.

The default settings generate a table with one sample per row and all the sample fields and SNPs in the columns.

Instead of displaying all fields in the samples table, the user can customize which of them have to be inserted in the file.

- SNP order

By default SNPs are ordered alfabetically. The user has the option also of ordering them by the Chromosome and Position fields in the SNPs table when this information has been inserted. (see Load dbSNP info for automatic filling of the table)

When this option is off, every sample takes one row and every SNP one column and in the corresponding cell their genotype can be found. In the case of diploid genotypes (usually most of them) it may be interesting to create two rows per sample or two columns per SNP and to separate the alleles of the genotype in two cells. The Split option allows to do this.

If the Split option is activated and there are haploid genotypes, the allele is written in the first cell and the second is left empty.

This is a fundamental time-saving feature. Selecting one of the fields in the Samples or SNP table, SNPator will run this process as many times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you have defined your samples in the "sex" field as "M" or "W", selecting "sex" as the attribute of the Sample batch mode will result in having two runs of the General report retrieving, taking separately men and women.

If you select at the same time sample and SNP batch fields, you are going to obtain as many runs of the analysis as all possible combinations of the values of samples and SNPs in the fields you selected.