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.
- Filling empty values with 'NA'
- Fields selection
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.
- Batch Mode:
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.