The Counts Table
howto_counts_table.RmdThis table stores the genetic information. An example of a correctly formatted Counts table is given below:
| study_id | survey_id | variant_string | variant_num | total_num | notes |
|---|---|---|---|---|---|
| Dama_2017 | Dama_2017_Bamako_2014 | crt:76:T | 130 | 170 | NA |
| Dama_2017 | Dama_2017_Bamako_2014 | mdr1:86:Y | 46 | 158 | NA |
| Asua_2019 | Asua_2019_Agago_2017 | k13:469:Y | 42 | 42 | NA |
| Asua_2019 | Asua_2019_Agago_2017 | k13:675:V | 42 | 42 | NA |
| Asua_2019 | Asua_2019_Arua_2017 | k13:675:V | 43 | 43 | NA |
| Asua_2019 | Asua_2019_Kole_2017 | k13:469:Y | 47 | 47 | NA |
| Asua_2019 | Asua_2019_Kole_2017 | k13:675:V | 47 | 47 | NA |
| Asua_2019 | Asua_2019_Lamwo_2017 | k13:469:Y | 43 | 43 | NA |
| Asua_2019 | Asua_2019_Lamwo_2017 | k13:675:V | 43 | 43 | NA |
| Asua_2019 | Asua_2019_Mubende_2017 | k13:469:F | 45 | 45 | NA |
Fields and requirements
Mandatory fields are shown in blue.
| Column | Type | Notes |
|---|---|---|
| study_id | Character string. Must be a valid identifier. | The foreign key for this study, pointing back to the Studies table. |
| survey_id | Character string. Must be a valid identifier. | The foreign key for this survey, pointing back to the Surveys table. |
| variant_string | Character string. A valid variantstring | A single- or multi-locus haplotype (see below). |
| variant_num | Numeric integer | The number of samples within which this variant was observed. |
| total_num | Numeric integer | The total number of samples successfully sequenced at this subset of loci. In other words, the number of samples that could have produced the observed variant. |
| notes | Character string | Any further information about this mutation (free text). |
variantstring format
The variantstring format is defined in the variantstring package - refer to that package documentation for details. The current version of STAVE uses variantstring v1.8.3.
The next page demonstrates some of the nuances of encoding genetic data.