read_qpcr: read_qpcr: a function to read the .xls files exported by...

In fishsciences/elaphos: Data Package For CFS E-DNA Experiments

read_qpcr: a function to read the .xls files exported by QuantStudio

Description

this takes a single .xls file as its input. It returns a dataframe.

Usage

read_qpcr(
  File,
  Cq_threshold = 40,
  Experiment,
  Keep_controls = FALSE,
  Column_numbers = c(2, 4, 5, 9),
  Column_names = c("WellPosition", "FilterID", "Target", "Cq"),
  Control_strings = c("NTC", "CT+", "^0$", "BHOO", "DS", "BHOO+", "DS+")
)

Arguments

File	the path to the .xls file
Cq_threshold	the Cq value at which to assume non-detection
Experiment	the name of the experiment or project associated with the qpcr data
Keep_controls	logical indicating whether you want to retain the FilterIDs with matching strings provided in the Control_strings argument
Column_numbers	integer vector corresponding to the columns you want to keep from the raw qpcr output
Column_names	character vector of column names to apply to the Column_numbers
Control_strings	character vector of strings to check for in the FilterID column that indicate a control sample

Value

a data frame with the following columns: "Experiment", "TechRep", "PlateID", "Control", and those specified in Column_names.

fishsciences/elaphos documentation built on July 9, 2022, 4:37 a.m.