parseClusterCounts {twoddpcr} | R Documentation

## Retain cluster counts and user-specified columns in data frames.

### Description

Take a data frame of droplet counts and returns only the raw "PP", "PN", "NP" and "NN" counts, plus any additional columns specified.

### Usage

    parseClusterCounts(
      df,
      rows = NULL,
      rowID = NULL,
      keepCols = NULL,
      keepColNames = NULL
    )

### Arguments

`df` | A data frame with droplet count columns in one of the following formats: `PP`, `PN`, `NP`, `NN`; `Ch1.Ch2.`, `Ch1.Ch2..1`, `Ch1.Ch2..2`, `Ch1.Ch2..3`; `Ch1+Ch2+`, `Ch1+Ch2-`, `Ch1-Ch2+`, `Ch1-Ch2-`; or `Ch1pCh2p`, `Ch1pCh2n`, `Ch1nCh2p`, `Ch1nCh2n`.
`rows` | A vector of rows (numbers or well names) to keep from the original data frame. If set to `NULL`, all wells will be used. Defaults to `NULL`.
`rowID` | If set, this field is used as the row names. If `NULL`, the existing row names from `df` are used. Defaults to `NULL`.
`keepCols` | A vector of columns to keep from `df`. If `NULL`, no extra columns are added. Defaults to `NULL`.
`keepColNames` | A vector of new column names for `keepCols`. If `NULL`, the column names from `keepCols` are reused. Defaults to `NULL`.

### Value

A data frame with the counts in the `PP`, `PN`, `PN` and `PN` convention.

### Author(s)

Anthony Chiu, anthony.chiu@cruk.manchester.ac.uk

### Examples

    ## Take a data frame with row names given by the well names. Get a simple
    ## count of droplets in each cluster.
    parseClusterCounts(KRAScounts)

    ## Keep only the row numbers 3, 6 and 9.
    parseClusterCounts(KRAScounts, rows=c(3, 6, 9))

    ## Keep only the rows labelled "F03", "A04", "D04".
    parseClusterCounts(KRAScounts, rows=c("F03", "A04", "D04"))

    ## Take a data frame with a 'Well' column and do the same as above.
    parseClusterCounts(KRAScountsWellCol, rowID="Well")

    ## Keep the 'InputAmount' column.
    parseClusterCounts(KRAScounts, keepCols=c("InputAmount"))

    ## Keep the 'InputAmount' column and rename it.
    parseClusterCounts(KRAScounts, keepCols=c("InputAmount"),
                       keepColNames=c("NanogramsIn"))

[Package twoddpcr version 1.18.0 Index]