Matrix QA

After every Matrix load or new Matrix generation, GWASpi will automatically generate 3 Quality Assurance reports:

Sample Missingness QA

This is a straight forward ratio calculation of missing genotypes versus total marker number in every given Sample:

Sample Missingness Ratio = (Nº of missing genotypes for Sample i) / (Total Nº of markers in this Matrix Marker Set)

Markers located in non-autosomal chromosomes in male Samples are counted as being homozygous.
See Matrix QA Reports section for details on table displays.

Marker Missingness QA

This is a straight forward ratio calculation of missing genotypes versus total sample number in any given Marker:

Marker Missingness Ratio = (Nº of missing genotypes for Marker i) / (Total Nº of samples in this Matrix Sample Set)

Markers located in non-autosomal chromosomes in male Samples are counted as being homozygous.
See Matrix QA Reports section for details on table displays.

Marker Mismatch QA

This QA checks if any Marker in the Marker Set has more than 2 alleles occurring in the current dataset. If yes, the marker will be labeled as mismatching.

Other Census Data

Additionally to the above QAs, GWASpi also performs a global genotype census count (AA, Aa or aa) on all Samples, regardless of their Case/Control Affection. Also, the major and minor alleles for every marker are calculated along their frequencies, as well as the encoding (ACGT, 1234, AB, 12) of the Matrix determined from the provided dataset.