maskAT {strvalidator}

Mask And Prepare Data To Analyze Analytical Threshold

Description

Break-out function to prepare data for the function calculateAT.

Usage

maskAT(
  data,
  ref = NULL,
  mask.height = TRUE,
  height = 500,
  mask.sample = TRUE,
  per.dye = TRUE,
  range.sample = 20,
  mask.ils = TRUE,
  range.ils = 10,
  ignore.case = TRUE,
  word = FALSE,
  debug = FALSE
)

Arguments

data

a data frame containing at least 'Dye.Sample.Peak', 'Sample.File.Name', 'Marker', 'Allele', 'Height', and 'Data.Point'.

ref

a data frame containing at least 'Sample.Name', 'Marker', 'Allele'.

mask.height

logical to indicate if high peaks should be masked.

height

integer for global lower peak height threshold for peaks to be excluded from the analysis. Active if 'mask.peak=TRUE.

mask.sample

logical to indicate if sample allelic peaks should be masked.

per.dye

logical TRUE if sample peaks should be masked per dye channel. FALSE if sample peaks should be masked globally across dye channels.

range.sample

integer to specify the masking range in (+/-) data points. Active if mask.sample=TRUE.

mask.ils

logical to indicate if internal lane standard peaks should be masked.

range.ils

integer to specify the masking range in (+/-) data points. Active if mask.ils=TRUE.

ignore.case

logical to indicate if sample matching should ignore case.

word

logical to indicate if word boundaries should be added before sample matching.

debug

logical to indicate if debug information should be printed.

Details

Prepares the 'SamplePlotSizingTable' for analysis of analytical threshold. It is needed by the plot functions for control of masking. The preparation consist of converting the 'Height' and 'Data.Point' column to numeric (if needed), then dye channel information is extracted from the 'Dye.Sample.Peak' column and added to its own 'Dye' column, known fragments of the internal lane standard (marked with an asterisk '*') is flagged as 'TRUE' in a new column 'ILS'.

Value

data.frame with added columns 'Dye' and 'ILS'.

See Also

calculateAT