Optimization develop clean check npx #318
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OlinkAnalyze/R/check_all_na_assays.R
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| #' Help function to identify assays with Only NAs | |||
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Help function to identify Olink assays with all quantified values NA.
| #' | ||
| #' @author | ||
| #' Simon Forsberg | ||
| #' Masoumeh Sheikhi |
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OlinkAnalyze/R/check_all_na_assays.R
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| #' Simon Forsberg | ||
| #' Masoumeh Sheikhi | ||
| #' @param df An arrow object containing columns OlinkID and | ||
| #' either NPX or Quantified_value |
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OlinkAnalyze/R/check_all_na_assays.R
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| #' Masoumeh Sheikhi | ||
| #' @param df An arrow object containing columns OlinkID and | ||
| #' either NPX or Quantified_value | ||
| #' @return A character vector of assays with all NA values. |
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A character vector containing OlinkID of assays with all quantified values NA.
OlinkAnalyze/R/check_all_na_assays.R
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| # Q2, when writing a test for this function, | ||
| # should we write a test for next line as well? | ||
| # seems like double testing for hidden internal functions..? | ||
| data_type <- detect_data_type(df) |
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detect_data_type will be replaced by the combination of the dictionary and detect_df_columns which determines the column names of the df.
Q1: Yes we can skip, but since we will be replacing this function call, I think we will need to add a check if df is an arrow object. We have such a function.
Q2: No, each function is tested on its own, so we do not need to retest them when we call them.
| # Check whether df contains NPX or QUANT ---- | ||
| if ("NPX" %in% df_colnames) { | ||
| data_type <- "NPX" | ||
| } else if ("Quantified_value" %in% df_colnames) { |
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do "grepl("Quantified", df_colnames)" instead of looking for an exact match.
| } else { | ||
| cli::cli_abort( | ||
| c( | ||
| "x" = "Neither NPX nor Quantified_value column present in the data."), |
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Please add quotations arounf NPX and Quantified_value
| df_colnames <- names(df) | ||
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| # Check whether df contains NPX or QUANT ---- | ||
| if ("NPX" %in% df_colnames) { |
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Also check that there is exactly 1 column name contaning NPX and only one column containing Quantified_value.
| #' | ||
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| # input is not an arrow object | ||
| test_that("detect_data_type detects that input is not an arrow object", { |
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Unneccesary to check.
| }) | ||
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| # Neither in dataset | ||
| test_that( |
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Test for multiple isntances of NPX or Quantified_value
some edits based on feedback provided by @klevdiamanti. More edits needs to be done. New files added: column_name_dict.R, column_name_dict.rda, check_column_names.R, detect_column_name.R and check_list.R column_name_dict.rda was createwd by data_raw
This update includes our work on our first hackathon. column_name_dict is updated, check_npx_col_names is added
Documentation added. Some tests added. More tests needed. Some other minor editing.
PR from Optimization develop to check npx to match most recent updates
sync some edits, tests will fail
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