parseClusterCounts: Retain cluster counts and user-specified columns in data...

In CRUKMI-ComputationalBiology/twoddpcr: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

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, [e-mail]

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"))

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