getfdata-method: Gets fluorescence data vectors from 'RDML' object

In RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

Description

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

Arguments

request	Output from AsTable method(RDML.AsTable)
dp.type	Type of fluorescence data (i.e. 'adp' for qPCR or 'mdp' for melting)
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.

Author(s)

Konstantin A. Blagodatskikh <[e-mail]>, Stefan Roediger <[e-mail]>, Michal Burdukiewicz <[e-mail]>

Examples

## Not run: 
## 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"),
                        dp.type = "adp")
## Show names for obtained fdata
colnames(fdata)

## End(Not run)

Example output

Loading experiment: All Wells
	run: Amp Step 3_FAM

	run: Amp Step 3_Cy5

Combining Bio-Rad runs

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

 [1] "cyc"                        "A07_katG 315_unkn_Cy5"     
 [3] "A07_katG 315_unkn_EvaGreen" "A08_katG 315_unkn_Cy5"     
 [5] "A08_katG 315_unkn_EvaGreen" "D07_katG 315_unkn_Cy5-2"   
 [7] "D07_katG 315_unkn_EvaGreen" "D08_katG 315_unkn_Cy5-2"   
 [9] "D08_katG 315_unkn_EvaGreen" "H07_katG 315_unkn_Cy5-2_rr"
[11] "H07_katG 315_unkn_EvaGreen" "H08_katG 315_unkn_Cy5-2_rr"
[13] "H08_katG 315_unkn_EvaGreen"

RDML documentation built on June 25, 2019, 5:03 p.m.