spectramaxImport: Import output files from Spectramax spectrophotometer

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

View source: R/spectramaxImport.R

Description

Import output files from Spectramax spectrophotometer (plate reader) into the list format compatible with the cellHTS2 package.

Usage

1
spectramaxImport(file, encoding="latin1")

Arguments

file

A Spectramax file

encoding

File character encoding, by default “latin1”

Details

The function imports output files from Spectramax plate reader, with which single-channel cell-based assays could be performed. Such assay includes WST-1 viability assay, which can be used to validate RTCA assay results.

Value

A list of two items: one data frame (no name) and one character vector (txt). The data frame contains following columns:

well

Well indices ([A-Z][0-9][0-9] format) on the microtitre plate

val

Value of each well

The character vector txt contains a copy of the file contents.

Author(s)

Jitao David Zhang <jitao_david.zhang@roche.com>

See Also

cellHTS2 package documentation.

Examples

1
2
3
4
5
6
7
8
9
wstFiles <- dir(system.file("extdata", package="RTCA"),
pattern="^WST.*csv$", full.names=TRUE)
spectramaxImport(wstFiles[1])

## NOT RUN
## spectramaxImport also supports multiple files, in which case the
## result is a list of individual lists
spectramaxImport(wstFiles)
## END NOT RUN

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: gtools
[[1]]
   well    val
1   A01 0.8418
2   A02 1.1461
3   A03 0.7507
4   A04 0.8919
5   A05 1.4515
6   A06 0.8852
7   A07 1.3086
8   A08 0.7005
9   A09 0.7103
10  A10 0.8516
11  A11 0.6629
12  A12 0.8230
13  B01 0.6564
14  B02 0.6347
15  B03 1.0209
16  B04 0.5768
17  B05 0.7648
18  B06 0.8500
19  B07 1.1708
20  B08 1.0678
21  B09 0.6044
22  B10 0.8102
23  B11 0.7272
24  B12 0.6461
25  C01 0.8059
26  C02 0.7071
27  C03 0.7196
28  C04 0.7801
29  C05 0.8277
30  C06 0.5966
31  C07 0.7307
32  C08 0.5555
33  C09 0.6208
34  C10 0.8486
35  C11 0.6674
36  C12 0.6908
37  D01 1.2612
38  D02 0.7967
39  D03 0.8734
40  D04 1.0377
41  D05 0.8368
42  D06 0.6960
43  D07 0.6227
44  D08 0.7018
45  D09 0.8157
46  D10 0.7835
47  D11 0.6195
48  D12 0.9039
49  E01 1.0698
50  E02 0.8368
51  E03 0.6195
52  E04 0.8238
53  E05 0.8109
54  E06 0.6351
55  E07 0.6762
56  E08 0.6154
57  E09 0.9764
58  E10 0.6738
59  E11 0.7268
60  E12 3.9097
61  F01 0.6948
62  F02 0.6303
63  F03 0.8006
64  F04 0.9147
65  F05 0.7392
66  F06 0.8870
67  F07 0.7461
68  F08 0.6141
69  F09 1.0231
70  F10 0.9180
71  F11 0.8580
72  F12 4.0000
73  G01 4.0000
74  G02 1.0807
75  G03 0.7954
76  G04 0.8813
77  G05 0.7510
78  G06 0.8683
79  G07 0.6575
80  G08 0.9138
81  G09 0.8857
82  G10 0.6024
83  G11 0.6968
84  G12 4.0000
85  H01 4.0000
86  H02 1.2625
87  H03 0.7272
88  H04 1.2100
89  H05 1.4784
90  H06 0.8508
91  H07 0.7486
92  H08 0.7804
93  H09 0.6331
94  H10 0.6729
95  H11 0.8374
96  H12 4.0000

$txt
 [1] "##BLOCKS= 1          "                                                                                     
 [2] "Plate:\tPlate#1\t1,1\tPlateFormat\tEndpoint\tAbsorbance\tRaw\tFALSE\t1\t\t\t\t\t\t1\t450\t1\t12\t96\t"     
 [3] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                              
 [4] "\t26,00\t0,8418\t1,1461\t0,7507\t0,8919\t1,4515\t0,8852\t1,3086\t0,7005\t0,7103\t0,8516\t0,6629\t0,823\t\t"
 [5] "\t\t0,6564\t0,6347\t1,0209\t0,5768\t0,7648\t0,85\t1,1708\t1,0678\t0,6044\t0,8102\t0,7272\t0,6461\t\t"      
 [6] "\t\t0,8059\t0,7071\t0,7196\t0,7801\t0,8277\t0,5966\t0,7307\t0,5555\t0,6208\t0,8486\t0,6674\t0,6908\t\t"    
 [7] "\t\t1,2612\t0,7967\t0,8734\t1,0377\t0,8368\t0,696\t0,6227\t0,7018\t0,8157\t0,7835\t0,6195\t0,9039\t\t"     
 [8] "\t\t1,0698\t0,8368\t0,6195\t0,8238\t0,8109\t0,6351\t0,6762\t0,6154\t0,9764\t0,6738\t0,7268\t3,9097\t\t"    
 [9] "\t\t0,6948\t0,6303\t0,8006\t0,9147\t0,7392\t0,887\t0,7461\t0,6141\t1,0231\t0,918\t0,858\t4\t\t"            
[10] "\t\t4\t1,0807\t0,7954\t0,8813\t0,751\t0,8683\t0,6575\t0,9138\t0,8857\t0,6024\t0,6968\t4\t\t"               
[11] "\t\t4\t1,2625\t0,7272\t1,21\t1,4784\t0,8508\t0,7486\t0,7804\t0,6331\t0,6729\t0,8374\t4\t\t"                
[12] "\t\t"                                                                                                      
[13] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                              
[14] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[15] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[16] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[17] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[18] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[19] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[20] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[21] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[22] "~End"                                                                                                      

[[1]]
[[1]][[1]]
   well    val
1   A01 0.8418
2   A02 1.1461
3   A03 0.7507
4   A04 0.8919
5   A05 1.4515
6   A06 0.8852
7   A07 1.3086
8   A08 0.7005
9   A09 0.7103
10  A10 0.8516
11  A11 0.6629
12  A12 0.8230
13  B01 0.6564
14  B02 0.6347
15  B03 1.0209
16  B04 0.5768
17  B05 0.7648
18  B06 0.8500
19  B07 1.1708
20  B08 1.0678
21  B09 0.6044
22  B10 0.8102
23  B11 0.7272
24  B12 0.6461
25  C01 0.8059
26  C02 0.7071
27  C03 0.7196
28  C04 0.7801
29  C05 0.8277
30  C06 0.5966
31  C07 0.7307
32  C08 0.5555
33  C09 0.6208
34  C10 0.8486
35  C11 0.6674
36  C12 0.6908
37  D01 1.2612
38  D02 0.7967
39  D03 0.8734
40  D04 1.0377
41  D05 0.8368
42  D06 0.6960
43  D07 0.6227
44  D08 0.7018
45  D09 0.8157
46  D10 0.7835
47  D11 0.6195
48  D12 0.9039
49  E01 1.0698
50  E02 0.8368
51  E03 0.6195
52  E04 0.8238
53  E05 0.8109
54  E06 0.6351
55  E07 0.6762
56  E08 0.6154
57  E09 0.9764
58  E10 0.6738
59  E11 0.7268
60  E12 3.9097
61  F01 0.6948
62  F02 0.6303
63  F03 0.8006
64  F04 0.9147
65  F05 0.7392
66  F06 0.8870
67  F07 0.7461
68  F08 0.6141
69  F09 1.0231
70  F10 0.9180
71  F11 0.8580
72  F12 4.0000
73  G01 4.0000
74  G02 1.0807
75  G03 0.7954
76  G04 0.8813
77  G05 0.7510
78  G06 0.8683
79  G07 0.6575
80  G08 0.9138
81  G09 0.8857
82  G10 0.6024
83  G11 0.6968
84  G12 4.0000
85  H01 4.0000
86  H02 1.2625
87  H03 0.7272
88  H04 1.2100
89  H05 1.4784
90  H06 0.8508
91  H07 0.7486
92  H08 0.7804
93  H09 0.6331
94  H10 0.6729
95  H11 0.8374
96  H12 4.0000

[[1]]$txt
 [1] "##BLOCKS= 1          "                                                                                     
 [2] "Plate:\tPlate#1\t1,1\tPlateFormat\tEndpoint\tAbsorbance\tRaw\tFALSE\t1\t\t\t\t\t\t1\t450\t1\t12\t96\t"     
 [3] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                              
 [4] "\t26,00\t0,8418\t1,1461\t0,7507\t0,8919\t1,4515\t0,8852\t1,3086\t0,7005\t0,7103\t0,8516\t0,6629\t0,823\t\t"
 [5] "\t\t0,6564\t0,6347\t1,0209\t0,5768\t0,7648\t0,85\t1,1708\t1,0678\t0,6044\t0,8102\t0,7272\t0,6461\t\t"      
 [6] "\t\t0,8059\t0,7071\t0,7196\t0,7801\t0,8277\t0,5966\t0,7307\t0,5555\t0,6208\t0,8486\t0,6674\t0,6908\t\t"    
 [7] "\t\t1,2612\t0,7967\t0,8734\t1,0377\t0,8368\t0,696\t0,6227\t0,7018\t0,8157\t0,7835\t0,6195\t0,9039\t\t"     
 [8] "\t\t1,0698\t0,8368\t0,6195\t0,8238\t0,8109\t0,6351\t0,6762\t0,6154\t0,9764\t0,6738\t0,7268\t3,9097\t\t"    
 [9] "\t\t0,6948\t0,6303\t0,8006\t0,9147\t0,7392\t0,887\t0,7461\t0,6141\t1,0231\t0,918\t0,858\t4\t\t"            
[10] "\t\t4\t1,0807\t0,7954\t0,8813\t0,751\t0,8683\t0,6575\t0,9138\t0,8857\t0,6024\t0,6968\t4\t\t"               
[11] "\t\t4\t1,2625\t0,7272\t1,21\t1,4784\t0,8508\t0,7486\t0,7804\t0,6331\t0,6729\t0,8374\t4\t\t"                
[12] "\t\t"                                                                                                      
[13] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                              
[14] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[15] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[16] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[17] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[18] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[19] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[20] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[21] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                  
[22] "~End"                                                                                                      


[[2]]
[[2]][[1]]
   well    val
1   A01 0.6909
2   A02 0.7777
3   A03 0.6789
4   A04 0.8947
5   A05 0.9559
6   A06 0.8031
7   A07 1.0867
8   A08 0.5962
9   A09 0.6286
10  A10 0.6615
11  A11 0.6923
12  A12 0.7713
13  B01 0.6220
14  B02 0.6381
15  B03 0.8448
16  B04 0.6431
17  B05 0.7317
18  B06 0.6570
19  B07 1.1038
20  B08 0.7921
21  B09 0.5948
22  B10 0.7926
23  B11 0.6992
24  B12 0.7124
25  C01 0.6260
26  C02 0.5985
27  C03 0.6633
28  C04 0.5649
29  C05 0.7042
30  C06 0.6174
31  C07 0.6151
32  C08 0.5732
33  C09 0.5746
34  C10 0.6847
35  C11 0.6010
36  C12 0.6467
37  D01 0.8067
38  D02 0.7343
39  D03 0.8928
40  D04 1.1655
41  D05 0.7490
42  D06 0.6335
43  D07 0.5354
44  D08 0.6514
45  D09 0.7788
46  D10 0.6458
47  D11 0.5899
48  D12 0.6491
49  E01 0.8322
50  E02 0.7243
51  E03 0.5818
52  E04 1.1071
53  E05 0.8134
54  E06 0.6617
55  E07 0.7217
56  E08 0.6346
57  E09 0.7907
58  E10 0.7367
59  E11 0.7503
60  E12 3.2344
61  F01 0.7017
62  F02 0.5943
63  F03 0.6206
64  F04 0.9087
65  F05 0.8079
66  F06 0.8056
67  F07 0.7029
68  F08 0.5198
69  F09 0.6621
70  F10 0.6964
71  F11 0.7311
72  F12 3.1705
73  G01 3.7214
74  G02 0.7721
75  G03 0.6879
76  G04 0.9567
77  G05 0.6829
78  G06 0.7044
79  G07 0.5764
80  G08 0.7579
81  G09 0.8166
82  G10 0.5758
83  G11 0.7845
84  G12 3.4257
85  H01 3.9439
86  H02 1.1261
87  H03 0.7129
88  H04 1.0079
89  H05 1.0756
90  H06 0.7270
91  H07 0.8401
92  H08 0.7087
93  H09 0.6357
94  H10 0.5935
95  H11 0.8831
96  H12 3.4315

[[2]]$txt
 [1] "##BLOCKS= 1          "                                                                                      
 [2] "Plate:\tPlate#1\t1,1\tPlateFormat\tEndpoint\tAbsorbance\tRaw\tFALSE\t1\t\t\t\t\t\t1\t450\t1\t12\t96\t"      
 [3] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                               
 [4] "\t26,00\t0,6909\t0,7777\t0,6789\t0,8947\t0,9559\t0,8031\t1,0867\t0,5962\t0,6286\t0,6615\t0,6923\t0,7713\t\t"
 [5] "\t\t0,622\t0,6381\t0,8448\t0,6431\t0,7317\t0,657\t1,1038\t0,7921\t0,5948\t0,7926\t0,6992\t0,7124\t\t"       
 [6] "\t\t0,626\t0,5985\t0,6633\t0,5649\t0,7042\t0,6174\t0,6151\t0,5732\t0,5746\t0,6847\t0,601\t0,6467\t\t"       
 [7] "\t\t0,8067\t0,7343\t0,8928\t1,1655\t0,749\t0,6335\t0,5354\t0,6514\t0,7788\t0,6458\t0,5899\t0,6491\t\t"      
 [8] "\t\t0,8322\t0,7243\t0,5818\t1,1071\t0,8134\t0,6617\t0,7217\t0,6346\t0,7907\t0,7367\t0,7503\t3,2344\t\t"     
 [9] "\t\t0,7017\t0,5943\t0,6206\t0,9087\t0,8079\t0,8056\t0,7029\t0,5198\t0,6621\t0,6964\t0,7311\t3,1705\t\t"     
[10] "\t\t3,7214\t0,7721\t0,6879\t0,9567\t0,6829\t0,7044\t0,5764\t0,7579\t0,8166\t0,5758\t0,7845\t3,4257\t\t"     
[11] "\t\t3,9439\t1,1261\t0,7129\t1,0079\t1,0756\t0,727\t0,8401\t0,7087\t0,6357\t0,5935\t0,8831\t3,4315\t\t"      
[12] "\t\t"                                                                                                       
[13] "\tTemperature(¡C)\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t\t"                                               
[14] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[15] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[16] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[17] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[18] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[19] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[20] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[21] "\t\t \t \t \t \t \t \t \t \t \t \t \t \t"                                                                   
[22] "~End"                                                                                                       

RTCA documentation built on Nov. 8, 2020, 7:52 p.m.