fullCountsSummary {twoddpcr} | R Documentation

## Take a data frame and compute the abundance of molecules.

### Description

Returns a data frame with basic counts, the concentration of each kind of target molecule, the ratio ch1:ch2 molecules, and the fractional abundance of ch1 molecules in the overall count.

### Usage

    fullCountsSummary(
      df,
      ch1Label = "Mt",
      ch2Label = "Wt",
      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`.
`ch1Label` | The prefix to use for the channel 1 target. Defaults to "Mt".
`ch2Label` | The prefix to use for the channel 2 target. Defaults to "Wt".
`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

- `rowID` as the row names (if given);

- the droplet counts per channel;

- the number of ch1 and ch2 positive and negative readings;

- the ch1 and ch2 concentration, copies per 20ul, and total copies per 20ul;

- the ratio of ch1 to ch2 molecules; and

- the fractional abundance of ch1 molecules in the overall molecule count (as a percentage).

### Author(s)

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

### Examples

    ## Take a data frame with row names given by the well names. Get estimates
    ## for the numbers of molecules in each sample..
    fullCountsSummary(KRAScounts)

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

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

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

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

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

[Package twoddpcr version 1.12.0 Index]