JoinPhenoAssay {pathwayPCA} | R Documentation

## Merge Phenotype and Assay Data by First Column (Sample ID)

### Description

Match the records from the phenotype data to the values in the assay data by sample ID. Return rows from each data frame with matches in both data frames. The sample ID must be the first column in both data frames.

### Usage

    JoinPhenoAssay(pheno_df, assay_df)

### Arguments

`pheno_df` | Phenotype data frame with the sample IDs in the first column
`assay_df` | Assay data frame with the sample IDs in the first column

### Details

Don't use this function. This is simply a wrapper around the `merge` function with extra checks for the class of the ID column. If you want to merge your two data frames by sample ID, you should use the `inner_join` function from the `dplyr` package instead. It's easier. See https://dplyr.tidyverse.org/reference/join.html.

### Value

A list of three elements:

- `assay` : A data frame with the rows from `assay_df` which are contained in `pheno_df`, ordered by their position in `pheno_df`.

- `response` : A data frame with the rows from `pheno_df` which are contained in `assay_df`.

- `sampleID` : A vector of the sample IDs shared by both data frames, ordered by their position in `pheno_df`.

### Examples

      # DO NOT CALL THIS FUNCTIONS DIRECTLY. USE CreateOmics() INSTEAD.

    ## Not run:
     data("colonSurv_df")
     JoinPhenoAssay(
       pheno_df = colonSurv_df[, 1:3],
       assay_df = colonSurv_df[, -(2:3)]
     )

    ## End(Not run)

[Package pathwayPCA version 1.2.0 Index]