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

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new-method: Creates new instance of 'RDML' class object

new-method: Creates new instance of 'RDML' class object
In RDML: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

Description Arguments Details Warning Author(s) Examples

Description

This function has been designed to import data from RDML v1.1 and v1.2 format files or from xls file generated by Applied Biosystems 7500. To import from xls this file have to contain Sample Setup and Multicomponent Data sheets!

Arguments

filename

string – path to file

show.progress

logical – show loading progress bar if TRUE

conditions.sep

separator for condition defined at sample name

format

string – input file format. Possible values auto, rdml, abi, excel, csv. See Details.

Details

File format options:

auto

Tries to detect format by extension. .xlsx – excel, .xls – abi, .csv – csv, other – rdml

abi

Reads .xls files generated by ABI 7500 v.2. To create such files use File>Export; check 'Sample Setup' and 'Multicomponent Data'; select 'One File'

excel

.xls or .xslx file with sheets 'description', 'adp', 'mdp'. See example file table.xlsx

csv

.csv file with first column 'cyc' or 'tmp' and fluorescence data in other columns

rdml

.rdml or .lc96p files

Warning

Although the format RDML claimed as data exchange format, the specific implementation of the format at devices from real manufacturers differ significantly. Currently this function is checked against RDML data from devices: Bio-Rad CFX96, Roche LightCycler 96 and Applied Biosystems StepOne.

Author(s)

Konstantin A. Blagodatskikh <k.blag@yandex.ru>, Stefan Roediger <stefan.roediger@b-tu.de>, Michal Burdukiewicz <michalburdukiewicz@gmail.com>

Examples

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## Not run: 
## Import from RDML file
PATH <- path.package("RDML")
filename <- paste(PATH, "/extdata/", "lc96_bACTXY.rdml", sep ="")
lc96 <- RDML$new(filename)

## Some kind of overview for lc96
lc96$AsTable(name.pattern = sample[[react$sample$id]]$description)
lc96$AsDendrogram()

## End(Not run)

Example output

Loading experiment: ca1eb225-ecea-4793-9804-87bfbb45f81d
	run: 65aeb1ec-b377-4ef6-b03f-92898d47488b
    fdata.name                               exp.id
 1:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 2:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 3:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 4:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 5:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 6:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 7:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 8:  Sample 39 ca1eb225-ecea-4793-9804-87bfbb45f81d
 9:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
10:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
11:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
12:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
13:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
14:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
15:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
16:  Sample 41 ca1eb225-ecea-4793-9804-87bfbb45f81d
17:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
18:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
19:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
20:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
21:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
22:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
23:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
24:  Sample 43 ca1eb225-ecea-4793-9804-87bfbb45f81d
25:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
26:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
27:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
28:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
29:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
30:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
31:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
32:  Sample 45 ca1eb225-ecea-4793-9804-87bfbb45f81d
33:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
34:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
35:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
36:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
37:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
38:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
39:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
40:  Sample 51 ca1eb225-ecea-4793-9804-87bfbb45f81d
41:  Sample 53 ca1eb225-ecea-4793-9804-87bfbb45f81d
42:  Sample 53 ca1eb225-ecea-4793-9804-87bfbb45f81d
43:  Sample 53 ca1eb225-ecea-4793-9804-87bfbb45f81d
44:  Sample 53 ca1eb225-ecea-4793-9804-87bfbb45f81d
45:  Sample 54 ca1eb225-ecea-4793-9804-87bfbb45f81d
46:  Sample 54 ca1eb225-ecea-4793-9804-87bfbb45f81d
47:  Sample 54 ca1eb225-ecea-4793-9804-87bfbb45f81d
48:  Sample 54 ca1eb225-ecea-4793-9804-87bfbb45f81d
49:  Sample 55 ca1eb225-ecea-4793-9804-87bfbb45f81d
50:  Sample 55 ca1eb225-ecea-4793-9804-87bfbb45f81d
51:  Sample 55 ca1eb225-ecea-4793-9804-87bfbb45f81d
52:  Sample 55 ca1eb225-ecea-4793-9804-87bfbb45f81d
53:  Sample 56 ca1eb225-ecea-4793-9804-87bfbb45f81d
54:  Sample 56 ca1eb225-ecea-4793-9804-87bfbb45f81d
55:  Sample 56 ca1eb225-ecea-4793-9804-87bfbb45f81d
56:  Sample 56 ca1eb225-ecea-4793-9804-87bfbb45f81d
57:  Sample 57 ca1eb225-ecea-4793-9804-87bfbb45f81d
58:  Sample 57 ca1eb225-ecea-4793-9804-87bfbb45f81d
59:  Sample 57 ca1eb225-ecea-4793-9804-87bfbb45f81d
60:  Sample 57 ca1eb225-ecea-4793-9804-87bfbb45f81d
61:  Sample 58 ca1eb225-ecea-4793-9804-87bfbb45f81d
62:  Sample 58 ca1eb225-ecea-4793-9804-87bfbb45f81d
63:  Sample 58 ca1eb225-ecea-4793-9804-87bfbb45f81d
64:  Sample 58 ca1eb225-ecea-4793-9804-87bfbb45f81d
    fdata.name                               exp.id
                                  run.id react.id position    sample target
 1: 65aeb1ec-b377-4ef6-b03f-92898d47488b       39      D03 Sample 39   bACT
 2: 65aeb1ec-b377-4ef6-b03f-92898d47488b       39      D03 Sample 39      X
 3: 65aeb1ec-b377-4ef6-b03f-92898d47488b       39      D03 Sample 39      Y
 4: 65aeb1ec-b377-4ef6-b03f-92898d47488b       39      D03 Sample 39    IPC
 5: 65aeb1ec-b377-4ef6-b03f-92898d47488b       40      D04 Sample 39   bACT
 6: 65aeb1ec-b377-4ef6-b03f-92898d47488b       40      D04 Sample 39      X
 7: 65aeb1ec-b377-4ef6-b03f-92898d47488b       40      D04 Sample 39      Y
 8: 65aeb1ec-b377-4ef6-b03f-92898d47488b       40      D04 Sample 39    IPC
 9: 65aeb1ec-b377-4ef6-b03f-92898d47488b       41      D05 Sample 41   bACT
10: 65aeb1ec-b377-4ef6-b03f-92898d47488b       41      D05 Sample 41      X
11: 65aeb1ec-b377-4ef6-b03f-92898d47488b       41      D05 Sample 41      Y
12: 65aeb1ec-b377-4ef6-b03f-92898d47488b       41      D05 Sample 41    IPC
13: 65aeb1ec-b377-4ef6-b03f-92898d47488b       42      D06 Sample 41   bACT
14: 65aeb1ec-b377-4ef6-b03f-92898d47488b       42      D06 Sample 41      X
15: 65aeb1ec-b377-4ef6-b03f-92898d47488b       42      D06 Sample 41      Y
16: 65aeb1ec-b377-4ef6-b03f-92898d47488b       42      D06 Sample 41    IPC
17: 65aeb1ec-b377-4ef6-b03f-92898d47488b       43      D07 Sample 43   bACT
18: 65aeb1ec-b377-4ef6-b03f-92898d47488b       43      D07 Sample 43      X
19: 65aeb1ec-b377-4ef6-b03f-92898d47488b       43      D07 Sample 43      Y
20: 65aeb1ec-b377-4ef6-b03f-92898d47488b       43      D07 Sample 43    IPC
21: 65aeb1ec-b377-4ef6-b03f-92898d47488b       44      D08 Sample 43   bACT
22: 65aeb1ec-b377-4ef6-b03f-92898d47488b       44      D08 Sample 43      X
23: 65aeb1ec-b377-4ef6-b03f-92898d47488b       44      D08 Sample 43      Y
24: 65aeb1ec-b377-4ef6-b03f-92898d47488b       44      D08 Sample 43    IPC
25: 65aeb1ec-b377-4ef6-b03f-92898d47488b       45      D09 Sample 45   bACT
26: 65aeb1ec-b377-4ef6-b03f-92898d47488b       45      D09 Sample 45      X
27: 65aeb1ec-b377-4ef6-b03f-92898d47488b       45      D09 Sample 45      Y
28: 65aeb1ec-b377-4ef6-b03f-92898d47488b       45      D09 Sample 45    IPC
29: 65aeb1ec-b377-4ef6-b03f-92898d47488b       46      D10 Sample 45   bACT
30: 65aeb1ec-b377-4ef6-b03f-92898d47488b       46      D10 Sample 45      X
31: 65aeb1ec-b377-4ef6-b03f-92898d47488b       46      D10 Sample 45      Y
32: 65aeb1ec-b377-4ef6-b03f-92898d47488b       46      D10 Sample 45    IPC
33: 65aeb1ec-b377-4ef6-b03f-92898d47488b       51      E03 Sample 51   bACT
34: 65aeb1ec-b377-4ef6-b03f-92898d47488b       51      E03 Sample 51      X
35: 65aeb1ec-b377-4ef6-b03f-92898d47488b       51      E03 Sample 51      Y
36: 65aeb1ec-b377-4ef6-b03f-92898d47488b       51      E03 Sample 51    IPC
37: 65aeb1ec-b377-4ef6-b03f-92898d47488b       52      E04 Sample 51   bACT
38: 65aeb1ec-b377-4ef6-b03f-92898d47488b       52      E04 Sample 51      X
39: 65aeb1ec-b377-4ef6-b03f-92898d47488b       52      E04 Sample 51      Y
40: 65aeb1ec-b377-4ef6-b03f-92898d47488b       52      E04 Sample 51    IPC
41: 65aeb1ec-b377-4ef6-b03f-92898d47488b       53      E05 Sample 53   bACT
42: 65aeb1ec-b377-4ef6-b03f-92898d47488b       53      E05 Sample 53      X
43: 65aeb1ec-b377-4ef6-b03f-92898d47488b       53      E05 Sample 53      Y
44: 65aeb1ec-b377-4ef6-b03f-92898d47488b       53      E05 Sample 53    IPC
45: 65aeb1ec-b377-4ef6-b03f-92898d47488b       54      E06 Sample 54   bACT
46: 65aeb1ec-b377-4ef6-b03f-92898d47488b       54      E06 Sample 54      X
47: 65aeb1ec-b377-4ef6-b03f-92898d47488b       54      E06 Sample 54      Y
48: 65aeb1ec-b377-4ef6-b03f-92898d47488b       54      E06 Sample 54    IPC
49: 65aeb1ec-b377-4ef6-b03f-92898d47488b       55      E07 Sample 55   bACT
50: 65aeb1ec-b377-4ef6-b03f-92898d47488b       55      E07 Sample 55      X
51: 65aeb1ec-b377-4ef6-b03f-92898d47488b       55      E07 Sample 55      Y
52: 65aeb1ec-b377-4ef6-b03f-92898d47488b       55      E07 Sample 55    IPC
53: 65aeb1ec-b377-4ef6-b03f-92898d47488b       56      E08 Sample 56   bACT
54: 65aeb1ec-b377-4ef6-b03f-92898d47488b       56      E08 Sample 56      X
55: 65aeb1ec-b377-4ef6-b03f-92898d47488b       56      E08 Sample 56      Y
56: 65aeb1ec-b377-4ef6-b03f-92898d47488b       56      E08 Sample 56    IPC
57: 65aeb1ec-b377-4ef6-b03f-92898d47488b       57      E09 Sample 57   bACT
58: 65aeb1ec-b377-4ef6-b03f-92898d47488b       57      E09 Sample 57      X
59: 65aeb1ec-b377-4ef6-b03f-92898d47488b       57      E09 Sample 57      Y
60: 65aeb1ec-b377-4ef6-b03f-92898d47488b       57      E09 Sample 57    IPC
61: 65aeb1ec-b377-4ef6-b03f-92898d47488b       58      E10 Sample 58   bACT
62: 65aeb1ec-b377-4ef6-b03f-92898d47488b       58      E10 Sample 58      X
63: 65aeb1ec-b377-4ef6-b03f-92898d47488b       58      E10 Sample 58      Y
64: 65aeb1ec-b377-4ef6-b03f-92898d47488b       58      E10 Sample 58    IPC
                                  run.id react.id position    sample target
    target.dyeId sample.type  adp   mdp
 1:          FAM         std TRUE FALSE
 2:          Hex         std TRUE FALSE
 3:    Texas Red         std TRUE FALSE
 4:          Cy5         std TRUE FALSE
 5:          FAM         std TRUE FALSE
 6:          Hex         std TRUE FALSE
 7:    Texas Red         std TRUE FALSE
 8:          Cy5         std TRUE FALSE
 9:          FAM         std TRUE FALSE
10:          Hex         std TRUE FALSE
11:    Texas Red         std TRUE FALSE
12:          Cy5         std TRUE FALSE
13:          FAM         std TRUE FALSE
14:          Hex         std TRUE FALSE
15:    Texas Red         std TRUE FALSE
16:          Cy5         std TRUE FALSE
17:          FAM         std TRUE FALSE
18:          Hex         std TRUE FALSE
19:    Texas Red         std TRUE FALSE
20:          Cy5         std TRUE FALSE
21:          FAM         std TRUE FALSE
22:          Hex         std TRUE FALSE
23:    Texas Red         std TRUE FALSE
24:          Cy5         std TRUE FALSE
25:          FAM         std TRUE FALSE
26:          Hex         std TRUE FALSE
27:    Texas Red         std TRUE FALSE
28:          Cy5         std TRUE FALSE
29:          FAM         std TRUE FALSE
30:          Hex         std TRUE FALSE
31:    Texas Red         std TRUE FALSE
32:          Cy5         std TRUE FALSE
33:          FAM         std TRUE FALSE
34:          Hex         std TRUE FALSE
35:    Texas Red         std TRUE FALSE
36:          Cy5         std TRUE FALSE
37:          FAM         std TRUE FALSE
38:          Hex         std TRUE FALSE
39:    Texas Red         std TRUE FALSE
40:          Cy5         std TRUE FALSE
41:          FAM        unkn TRUE FALSE
42:          Hex        unkn TRUE FALSE
43:    Texas Red        unkn TRUE FALSE
44:          Cy5        unkn TRUE FALSE
45:          FAM        unkn TRUE FALSE
46:          Hex        unkn TRUE FALSE
47:    Texas Red        unkn TRUE FALSE
48:          Cy5        unkn TRUE FALSE
49:          FAM        unkn TRUE FALSE
50:          Hex        unkn TRUE FALSE
51:    Texas Red        unkn TRUE FALSE
52:          Cy5        unkn TRUE FALSE
53:          FAM        unkn TRUE FALSE
54:          Hex        unkn TRUE FALSE
55:    Texas Red        unkn TRUE FALSE
56:          Cy5        unkn TRUE FALSE
57:          FAM        unkn TRUE FALSE
58:          Hex        unkn TRUE FALSE
59:    Texas Red        unkn TRUE FALSE
60:          Cy5        unkn TRUE FALSE
61:          FAM        unkn TRUE FALSE
62:          Hex        unkn TRUE FALSE
63:    Texas Red        unkn TRUE FALSE
64:          Cy5        unkn TRUE FALSE
    target.dyeId sample.type  adp   mdp
Warning message:
In lc96$AsTable(name.pattern = sample[[react$sample$id]]$description) :
  fdata.name column has duplicates! Try another name.pattern.
'dendrogram' with 1 branches and 8 members total, at height 5

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

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