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Add New Phenotypes

Select the zip file bundle containing information on the phenotypes you wish to upload, then click the "Upload Phenotypes" button below to upload the data.

See the File Formats section below to get an understanding of what is expected of the bundle files you upload.

This will not update any existing phenotypes!

File Formats

We accept an extended form of the input files' format used with the R/qtl2 software as a single ZIP file

The files that are used for this feature are:

Other files within the bundle will be ignored, for this feature.

The following section will detail the expectations for each of the different file types within the uploaded ZIP file bundle for phenotypes:

Control File

There MUST be one, and only one file that acts as the control file. This file can be:

The control file is useful for defining things about the bundle such as:

pheno File(s)

These files are the main data files. You must have at least one of these files in your bundle for it to be valid for this step.

The data is a matrix of individuals × phenotypes by default, as below:
id,10001,10002,10003,10004,…
BXD1,61.400002,54.099998,483,49.799999,…
BXD2,49,50.099998,403,45.5,…
BXD5,62.5,53.299999,501,62.900002,…
BXD6,53.099998,55.099998,403,NA,…

If the pheno_transposed value is set to True, then the data will be a phenotypes × individuals matrix as in the example below:
id,BXD1,BXD2,BXD5,BXD6,…
10001,61.400002,49,62.5,53.099998,…
10002,54.099998,50.099998,53.299999,55.099998,…
10003,483,403,501,403,…
10004,49.799999,45.5,62.900002,NA,…

phenocovar File(s)

At least one phenotypes metadata file with the metadata values such as descriptions, PubMed Identifier, publication titles (if present), etc.

The data in this/these file(s) is a matrix of phenotypes × phenotypes-covariates. The first column is always the phenotype names/identifiers — same as in the R/qtl2 format.

phenocovar files should never be transposed!

This file MUST be present in the bundle, and have data for the bundle to be considered valid by our system for this step.
In addition to that, the following are the fields that must be present, and have values, in the file before the file is considered valid:

The following optional fields can also be provided:

These files will be marked up in the control file with the phenocovar key, as in the examples below:

  1. JSON: single file
    {
      ⋮,
      "phenocovar": "your_covariates_file.csv",
      ⋮
    }
  2. JSON: multiple files
    {
      ⋮,
      "phenocovar": [
        "covariates_file_01.csv",
        "covariates_file_01.csv",
        ⋮
      ],
      ⋮
    }
  3. YAML: single file or

    phenocovar: your_covariates_file.csv
  4. YAML: multiple files

    phenocovar:
    - covariates_file_01.csv
    - covariates_file_02.csv
    - covariates_file_03.csv

phenose and phenonum File(s)

These are extensions to the R/qtl2 standard, i.e. these types ofs file are not supported by the original R/qtl2 file format

We use these files to upload the standard errors (phenose) when the data file (pheno) is average data. In that case, the phenonum file(s) contains the number of individuals that were involved when computing the averages.

Both types of files are matrices of individuals × phenotypes by default. Like the related pheno files, if pheno_transposed: True, then the file will be a matrix of phenotypes × individuals.

Notes for Devs (well… Fred, really.)

Use the following resources for automated retrieval of certain data

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