calculateSlope: Calculate Profile Slope.

Description

Calculate profile slope for samples.

Usage

calculateSlope(data, ref, conf = 0.975, kit = NULL, debug = FALSE, ...)

Arguments

data

data.frame with at least columns 'Sample.Name', 'Marker', and 'Height'.

ref

data.frame with at least columns 'Sample.Name', 'Marker', and 'Allele'

conf

numeric confidence limit to calculate a confidence interval from (Student t Distribution with 'Peaks'-2 degree of freedom). Default is 0.975 corresponding to a 95% confidence interval.

kit

character string or vector specifying the analysis kits used to produce the data. If length(kit) != number of groups, kit[1] will be used for all groups.

debug

logical indicating printing debug information.

...

additional arguments for filterProfile function

Value

data.frame with with columns 'Sample.Name', 'Kit', 'Group', 'Slope', 'Error', 'Peaks', 'Lower', and 'Upper'.

Details

Calculates the profile slope for each sample. The slope is calculated as a linear model specified by the response (natural logarithm of peak height) by the term size (in basepair). If 'Size' is not present in the dataset, one or multiple kit names can be given as argument 'kit'. The specified kits will be used to estimate the size of each allele. If 'kit' is NULL the kit(s) will be autodetected, and the 'Size' will be calculated.

The column 'Group' can be used to separate datasets to be compared, and if so 'kit' must be a vector of equal length as the number of groups, and in the same order. If not the first 'kit' will be recycled for all groups.

Data will be filtered using the reference profiles.