RDML (version 0.8-3)

GetFData: Gets fluorescence data vectors from RDML object

Description

Gets fluorescence data vectors from RDML object for specified method of experiment.

Arguments

request

Output from AsTable method(RDML.AsTable)

limits

vector with two values (min and max values) that limits cycles or temperature that should be gotten. If this values are smaller or bigger than min or max values at dats - NAwill be used nearest available fluorescence data.

data.type

Type of fluorescence data (i.e. 'adp' for qPCR or 'mdp' for melting)

first.col.name

name of the column that contains constant data for all samples (i.e. for 'adp' it can be 'cyc' or 'tmp' as described at RDML v1.2 standard)

long.table

Output table is ready for ggplot (See RDML.AsTable for example)

Value

• matrix which contains selected fluorescence data and additional information fromm request if long.table = TRUE.

Examples

## internal dataset BioRad_qPCR_melt.rdml (in 'data' directory)
## generated by Bio-Rad CFX96. Contains qPCR and melting data.
## Import without splitting by targets/types and with
## custom name pattern.
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "BioRad_qPCR_melt.rdml", sep ="")
cfx96 <- RDML$new(filename)
## Select melting fluorescence data with sample.type 'unkn'.
library(dplyr)
tab <- cfx96$AsTable()
fdata <- cfx96$GetFData(filter(tab, sample.type == "unkn"),
                        limit
                        data.type = "mdp")
## Show names for getted fdata
colnames(fdata)