prep: Create cqdat object
In edpcr: Performs Extended Digital PCR Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Creates cqdat object from data frame containing x-location, y-location and Cq values, or from a vector just containing Cq values

1 2	prep(data, failcode = NA, cq.xlim = NA, out = c(3.5, 5), h = NA)

`data`	data frame of Cq data with locations containing colnames "cq","x" and "y", or a vector of Cq data.
`failcode`	either NA, number, character string: designation of negative partitions within cq column
`cq.xlim`	if NA then no columns trimmed, if vector then `cq.xlim` is the start and end columns for which Cq data is retained, with positive and negative counts only kept for remaining trimmed columns.
`out`	vector of 2 positive numbers defining distance from mean (after detrending) for excluding low and high outliers respectively
`h`	threshold value

Where there are spurious trends in the Cq data at the edges of the panel they may be considered unreliable. The cq.xlim argument permits columns to be censored where the partitions with Cq values are treated as having at least 1 molecule. The number of such partitions is codent1, with the negative partitions from the censored columns being codent0.

There may also be values that are considered outliers for being too low or too high. Through the out these outliers can be censored, with the associated counts n.lo and coden.hi respectively. They are considered to represent more than 1 initial molecule and exactly 1 initial molecule respectively.

A list with the class "cqdat" and the components:

`data`	matrix of Cq data, excluding negative partitions
`h`	threshold value
`n0, n1, nt0, nt1, n.lo, n.hi`	counts
`nx, ny`	numbers of columns and rows

Philip Wilson

fetch

dat<-cbind(x=rep(1:4,each=3),
           y=rep(1:3,times=4),
           cq=c(22.859,21.638,24.152,999,   
                29.081,23.817,23.930,23.943,
                22.934,23.473,999,22.819))
cqdata<-prep(dat,failcode=999,cq.xlim=c(1,2),h=.05)