| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-01-16 | Provide defaults for various control variables...`na.strings` has a default value of "NA" as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#CSV_files quote: > Missing value codes will be specified in the control file (as > na.strings, with default value "NA") and will apply across all > files, so a missing value code for one file cannot be an allowed > value in another file. for `comment.char` > The CSV files can include a header with a set of comment lines > initiated by a value specified in the control file as comment.char > (with default value "#"). for `sep`: The default separator is expected to be the comma, as stated in https://kbroman.org/qtl2/assets/vignettes/input_files.html#field-separator quote: > If the data files use a separator other than a comma ... | Frederick Muriuki Muriithi |
| 2024-01-15 | Process `na.strings` even for default cases...There was a bug where the `na.strings` were not processed correctly if the user called the `r_qtl.r_qtl2.file_data(...)` function without explicitly providing the `process_*` arguments. This commit fixes that. | Frederick Muriuki Muriithi |
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi |
| 2024-01-10 | Provide convenience functions to avoid subtle call errors | Frederick Muriuki Muriithi |
| 2024-01-10 | Make identifier column name explicit...Since the R/qtl2 bundle generator could name the identifier column anything, this commit converts the incoming identifier column name into something explicit that we know and can use. | Frederick Muriuki Muriithi |
| 2024-01-09 | Raise exception on reading non-existing file...The validation checks ensure that whatever files are listed in the control file exist in the zip file bundle. It is still possible, however, that the code tries to read a file that does not exist in the file and is not listed in the control file. In those cases, raise the appropriate exception. | Frederick Muriuki Muriithi |
| 2024-01-08 | Upload R/qtl2 zip bundle and check for errors. | Frederick Muriuki Muriithi |
| 2024-01-04 | Parse sex information from R/qtl bundle. | Frederick Muriuki Muriithi |
| 2024-01-04 | Parse cross information from R/qtl2 bundle. | Frederick Muriuki Muriithi |
| 2024-01-04 | Process sex and cross information data in "covar" files. | Frederick Muriuki Muriithi |
| 2024-01-04 | Parse multiple files with same file key. | Frederick Muriuki Muriithi |
| 2024-01-03 | Use generic parser. Remove obsoleted functions. | Frederick Muriuki Muriithi |
| 2024-01-03 | Parse founder_geno files. Generalise parsing files....* Add tests for parsing "founder_geno" files * Extract common file parsing structure out to more general function * Use generic function to parse "founder_geno" file in test | Frederick Muriuki Muriithi |
| 2024-01-03 | Parse the phenotype data from the R/qtl2 bundle. | Frederick Muriuki Muriithi |
| 2024-01-03 | Rename argument and add documentation to functions. | Frederick Muriuki Muriithi |
| 2024-01-03 | Extract processing of transposed files into reusable function....The processing of transposed files is similar across files. This commit extracts the common parts into a separate function. | Frederick Muriuki Muriithi |
| 2024-01-03 | Refactor: Extract potentially reusable functions...The processing of transposed files is probably going to be very similar, thus the need to extract some reusable code from the geno-file-specific function in preparation. | Frederick Muriuki Muriithi |
| 2024-01-02 | Abstract away non-transposed file processing...Since the processing of non-transposed files is mostly similar, abstract away the common operations into a separate function and use the function instead of repeating the same pattern of code throughout the codebase. | Frederick Muriuki Muriithi |
| 2024-01-02 | Cleanup: Fix linting and typing errors and update docs. | Frederick Muriuki Muriithi |
| 2023-12-28 | Rework parsing of transposed geno files. | Frederick Muriuki Muriithi |
| 2023-12-28 | Handle transposed geno files. | Frederick Muriuki Muriithi |
| 2023-12-27 | Tests: Test parsing of non-transposed geno files....Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files. | Frederick Muriuki Muriithi |
| 2023-12-27 | Tests: Add tests for parsing gmap files. | Frederick Muriuki Muriithi |
| 2023-12-25 | Generalise to read both genetic and physical maps. | Frederick Muriuki Muriithi |
| 2023-12-25 | Read genetic map files | Frederick Muriuki Muriithi |
| 2023-12-20 | Read genotype files | Frederick Muriuki Muriithi |
| 2023-12-20 | Read R/qtl2 format files...* Set up error objects. * Read the control data. | Frederick Muriuki Muriithi |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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