fullCountsSummary: Take a data frame and compute the abundance of molecules.

In CRUKMI-ComputationalBiology/twoddpcr: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting 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, [e-mail]

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"))

CRUKMI-ComputationalBiology/twoddpcr documentation built on Feb. 14, 2021, 9:18 p.m.