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diff --git a/doc/file-formats.md b/doc/file-formats.md index 52ccd0a..8515b38 100644 --- a/doc/file-formats.md +++ b/doc/file-formats.md @@ -47,6 +47,27 @@ chr11 3462348 T -0.361 -0.3244 -0.326 0.0986 chr11 3464016 A -0.3461 -0.334 -0.3331 0.08 ``` +## phenotype (and covariates) file + +The phenotype file is a tab-separated values (TSV) file. The first line MUST be a header with column labels. Each row corresponds to one individual. The column labelled `sample-id` contains the sample identifier for that individual. Other columns each contain a phenotypical trait for that individual. The headers of these columns MUST be the names of the phenotypes. Column headers are case-sensitive. + +Here is an example phenotype file. +``` +sample-id sex start-weight end-weight weight-growth-slope glucose-weight +A063361614 1 -0.07717 0.04008 0.09186 0.0006918 +A084271874 1 -0.09059 -0.1205 -0.02113 -0.1259 +A048102344 1 -0.08586 -0.04292 0.03724 -0.05113 +A048120064 1 -0.09509 -0.04183 -0.0003283 -0.05509 +A083583043 1 0.06565 0.02807 -0.02835 0.02076 +A063014029 1 -0.1015 -0.113 -0.02167 -0.1116 +A063001812 1 0.1294 0.1109 0.0217 0.1099 +A063873017 1 0.1711 0.1519 0.0116 0.1564 +A066790098 1 0.04236 0.2847 0.1172 0.2834 +A053042270 1 0.1332 0.1758 0.05178 0.2161 +``` + +Phenotype files may also be used to store covariates. + ## key file The key file is a tab-separated values (TSV) file with numerical data. There MUST be no column headers. |