Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Class to Contain GS Reference Mapper OutputDescriptionContainer to store data imported from a project of Roche's GS Reference Mapper Software. It stores all information into a Biobase ExpressionSet. Objects from the ClassObjects can be created by calls of the form Slots
ExtendsClass Methods
Author(s)Christoph Bartenhagen See Also
Examples
# sum up class structure
showClass("MapperSet")
# load a GS Mapper dataset containing 3 samples and 111 variants
data(mapperSetExample)
mapperSetExample
# show contents of assay, feature and pheno data
assayData(mapperSetExample)
fData(mapperSetExample)
pData(mapperSetExample)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(R453Plus1Toolbox)
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R453Plus1Toolbox/MapperSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MapperSet-class
> ### Title: Class to Contain GS Reference Mapper Output
> ### Aliases: MapperSet-class annotateVariants,MapperSet-method
> ### htmlReport,MapperSet-method setVariantFilter,MapperSet-method
> ### getVariantPercentages,MapperSet-method getReadStatus
> ### getReadStatus,MapperSet-method
> ### Keywords: classes
>
> ### ** Examples
>
>
> # sum up class structure
> showClass("MapperSet")
Class "MapperSet" [package "R453Plus1Toolbox"]
Slots:
Name: variantFilterPerc variantFilter dirs
Class: numeric character character
Name: assayData phenoData featureData
Class: AssayData AnnotatedDataFrame AnnotatedDataFrame
Name: experimentData annotation protocolData
Class: MIAxE character AnnotatedDataFrame
Name: .__classVersion__
Class: Versions
Extends:
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
>
> # load a GS Mapper dataset containing 3 samples and 111 variants
> data(mapperSetExample)
> mapperSetExample
MapperSet (storageMode: list)
assayData: 111 features, 3 samples
element names: variantForwCount, totalForwCount, variantRevCount, totalRevCount
protocolData: none
phenoData
sampleNames: N01 N03 N04
varLabels: accessionNumber
varMetadata: labelDescription
featureData
featureNames: 1 2 ... 111 (111 total)
fvarLabels: chr strand ... knownSNP (8 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>
> # show contents of assay, feature and pheno data
> assayData(mapperSetExample)
$variantForwCount
N01 N03 N04
1 9 7 7
2 9 6 6
3 11 3 5
4 7 5 11
5 8 5 6
6 11 5 9
7 11 4 7
8 8 5 5
9 4 2 7
10 8 0 2
11 1 4 0
12 4 5 0
13 8 8 4
14 13 9 4
15 2 3 0
16 1 0 0
17 3 0 0
18 11 13 12
19 7 4 7
20 4 2 3
21 8 6 7
22 13 9 16
23 5 4 0
24 5 4 0
25 4 0 9
26 6 0 7
27 16 10 14
28 7 0 0
29 13 10 15
30 3 1 2
31 8 0 0
32 11 6 5
33 8 7 1
34 2 0 1
35 7 0 0
36 2 1 0
37 4 0 0
38 1 0 0
39 3 0 1
40 19 13 20
41 7 6 16
42 10 6 16
43 9 5 12
44 11 9 16
45 3 4 8
46 5 3 6
47 2 0 0
48 2 0 0
49 15 14 16
50 11 6 14
51 4 0 2
52 4 0 0
53 3 0 5
54 5 1 0
55 1 0 0
56 8 0 0
57 2 0 0
58 6 0 0
59 0 4 0
60 0 3 0
61 0 3 0
62 0 3 0
63 0 2 0
64 0 4 0
65 0 3 0
66 0 8 0
67 0 3 0
68 0 3 0
69 0 2 0
70 0 2 0
71 0 3 0
72 0 4 0
73 0 7 0
74 0 3 0
75 0 3 0
76 0 8 0
77 0 1 0
78 0 5 0
79 0 7 0
80 0 2 0
81 0 4 0
82 0 4 0
83 0 9 0
84 0 6 0
85 0 3 0
86 0 2 0
87 0 4 0
88 0 28 9
89 0 4 0
90 0 5 5
91 0 2 0
92 0 0 6
93 0 0 11
94 0 0 6
95 0 0 7
96 0 0 3
97 0 0 12
98 0 0 4
99 0 0 6
100 0 0 2
101 0 0 5
102 0 0 5
103 0 0 5
104 0 0 1
105 0 0 10
106 0 0 10
107 0 0 2
108 0 0 2
109 0 0 14
110 0 0 3
111 0 0 2
$totalForwCount
N01 N03 N04
1 9 7 7
2 9 6 6
3 11 5 5
4 7 7 11
5 8 5 6
6 11 6 9
7 12 9 7
8 8 5 5
9 7 6 7
10 8 0 2
11 7 6 0
12 13 9 0
13 9 9 8
14 13 9 9
15 12 14 0
16 5 0 0
17 9 0 0
18 11 13 12
19 9 4 7
20 4 2 3
21 8 6 7
22 16 10 19
23 6 4 0
24 6 4 0
25 13 0 9
26 9 0 9
27 16 10 14
28 19 0 0
29 13 10 15
30 3 1 2
31 16 0 0
32 11 6 5
33 12 7 5
34 9 0 2
35 16 0 0
36 2 1 0
37 5 0 0
38 9 0 0
39 5 0 5
40 19 13 20
41 13 6 16
42 15 6 16
43 9 5 12
44 16 9 16
45 5 4 8
46 5 3 6
47 13 0 0
48 13 0 0
49 16 14 16
50 11 6 14
51 8 0 5
52 9 0 0
53 8 0 7
54 10 6 0
55 10 0 0
56 17 0 0
57 8 0 0
58 13 0 0
59 0 6 0
60 0 8 0
61 0 7 0
62 0 6 0
63 0 4 0
64 0 5 0
65 0 4 0
66 0 14 0
67 0 6 0
68 0 4 0
69 0 15 0
70 0 11 0
71 0 8 0
72 0 5 0
73 0 11 0
74 0 4 0
75 0 13 0
76 0 14 0
77 0 5 0
78 0 5 0
79 0 7 0
80 0 7 0
81 0 7 0
82 0 11 0
83 0 15 0
84 0 10 0
85 0 5 0
86 0 6 0
87 0 4 0
88 0 28 13
89 0 7 0
90 0 5 7
91 0 5 0
92 0 0 14
93 0 0 17
94 0 0 16
95 0 0 16
96 0 0 16
97 0 0 23
98 0 0 5
99 0 0 13
100 0 0 19
101 0 0 15
102 0 0 8
103 0 0 20
104 0 0 4
105 0 0 19
106 0 0 10
107 0 0 3
108 0 0 3
109 0 0 14
110 0 0 9
111 0 0 6
$variantRevCount
N01 N03 N04
1 8 6 2
2 8 3 1
3 10 2 8
4 8 2 5
5 8 11 3
6 4 3 6
7 8 2 8
8 5 3 9
9 3 1 7
10 3 0 6
11 4 3 0
12 3 6 0
13 10 11 5
14 7 12 6
15 2 2 0
16 2 0 0
17 2 0 0
18 5 13 12
19 8 10 8
20 2 1 3
21 13 1 9
22 19 10 15
23 1 2 0
24 2 2 0
25 1 0 7
26 4 0 5
27 7 5 8
28 5 0 0
29 22 15 14
30 2 2 2
31 4 0 0
32 8 7 4
33 3 7 6
34 1 0 4
35 4 0 0
36 1 3 0
37 10 0 0
38 2 0 0
39 1 0 3
40 13 6 19
41 8 10 12
42 9 7 13
43 11 7 6
44 6 8 16
45 8 8 9
46 12 10 10
47 2 0 0
48 3 0 0
49 17 10 22
50 15 11 12
51 4 0 3
52 3 0 0
53 10 0 3
54 5 6 0
55 7 0 0
56 6 0 0
57 3 0 0
58 4 0 0
59 0 2 0
60 0 4 0
61 0 3 0
62 0 2 0
63 0 1 0
64 0 2 0
65 0 1 0
66 0 3 0
67 0 3 0
68 0 3 0
69 0 1 0
70 0 2 0
71 0 2 0
72 0 2 0
73 0 6 0
74 0 3 0
75 0 2 0
76 0 2 0
77 0 5 0
78 0 1 0
79 0 8 0
80 0 6 0
81 0 6 0
82 0 2 0
83 0 7 0
84 0 6 0
85 0 4 0
86 0 2 0
87 0 1 0
88 0 14 7
89 0 9 0
90 0 7 1
91 0 1 0
92 0 0 9
93 0 0 9
94 0 0 3
95 0 0 4
96 0 0 1
97 0 0 10
98 0 0 3
99 0 0 4
100 0 0 1
101 0 0 3
102 0 0 3
103 0 0 6
104 0 0 3
105 0 0 3
106 0 0 8
107 0 0 2
108 0 0 2
109 0 0 8
110 0 0 2
111 0 0 3
$totalRevCount
N01 N03 N04
1 8 6 2
2 8 3 1
3 10 4 8
4 8 7 5
5 8 11 3
6 4 3 6
7 10 7 8
8 5 3 9
9 5 4 7
10 3 0 6
11 7 4 0
12 10 13 0
13 11 11 12
14 8 12 10
15 7 3 0
16 3 0 0
17 6 0 0
18 5 13 12
19 15 10 8
20 2 1 3
21 13 1 9
22 19 11 16
23 1 3 0
24 2 3 0
25 10 0 7
26 5 0 12
27 7 5 9
28 9 0 0
29 22 15 14
30 2 2 2
31 12 0 0
32 8 7 4
33 5 7 11
34 9 0 8
35 12 0 0
36 1 3 0
37 11 0 0
38 8 0 0
39 5 0 7
40 14 6 19
41 16 10 12
42 14 7 13
43 11 7 6
44 9 8 16
45 14 8 10
46 12 10 10
47 13 0 0
48 13 0 0
49 19 10 22
50 15 11 12
51 10 0 8
52 12 0 0
53 14 0 8
54 14 11 0
55 20 0 0
56 18 0 0
57 11 0 0
58 13 0 0
59 0 7 0
60 0 6 0
61 0 5 0
62 0 4 0
63 0 3 0
64 0 3 0
65 0 2 0
66 0 9 0
67 0 7 0
68 0 4 0
69 0 13 0
70 0 8 0
71 0 5 0
72 0 8 0
73 0 10 0
74 0 11 0
75 0 4 0
76 0 5 0
77 0 9 0
78 0 2 0
79 0 8 0
80 0 12 0
81 0 9 0
82 0 4 0
83 0 13 0
84 0 12 0
85 0 9 0
86 0 5 0
87 0 1 0
88 0 14 12
89 0 12 0
90 0 8 3
91 0 2 0
92 0 0 18
93 0 0 15
94 0 0 16
95 0 0 17
96 0 0 17
97 0 0 16
98 0 0 6
99 0 0 8
100 0 0 10
101 0 0 9
102 0 0 8
103 0 0 16
104 0 0 8
105 0 0 7
106 0 0 8
107 0 0 3
108 0 0 2
109 0 0 8
110 0 0 2
111 0 0 8
> fData(mapperSetExample)
chr strand start end referenceBases variantBase regName
1 1 + 11846252 11846252 G A MTHFR
2 1 + 11846447 11846447 G A MTHFR
3 1 + 11847340 11847340 --- AGA MTHFR
4 1 + 11847759 11847759 C T MTHFR
5 1 + 11848879 11848879 A G MTHFR
6 1 + 11849447 11849447 A G MTHFR
7 1 + 11850365 11850365 T G MTHFR
8 1 + 11854457 11854457 G A MTHFR
9 1 + 11854755 11854755 G A MTHFR
10 1 + 11856378 11856378 G A MTHFR
11 1 + 16242620 16242620 C A SPEN
12 1 + 16255644 16255644 C T SPEN
13 1 + 16256007 16256007 T C SPEN
14 1 + 16259813 16259813 A G SPEN
15 1 + 16260916 16260916 C T SPEN
16 1 + 16262404 16262404 C T SPEN
17 1 + 16263708 16263708 C T SPEN
18 1 + 47682017 47682017 T G TAL1
19 1 + 47684677 47684677 T G TAL1
20 1 + 47685455 47685455 T C TAL1
21 1 + 47716043 47716044 AA -- STIL
22 1 + 47717189 47717189 A G STIL
23 1 + 97543752 97543752 G A DPYD
24 1 + 97543764 97543764 C T DPYD
25 1 + 97544258 97544258 A G DPYD
26 1 + 97981395 97981395 T C DPYD
27 1 + 98185527 98185527 A G DPYD
28 1 + 98185720 98185723 TCAC ---- DPYD
29 1 + 98186077 98186077 T C DPYD
30 1 + 98348885 98348885 G A DPYD
31 1 + 115249843 115249843 G A NRAS
32 1 + 164789444 164789444 A G PBX1
33 1 + 186265948 186265948 T A PRG4
34 1 + 186273994 186273994 C T PRG4
35 1 + 186275760 186275760 G A PRG4
36 1 + 186277088 186277088 G C PRG4
37 10 + 27036912 27036912 ----- TCTTT ABI1
38 10 + 27040636 27040638 TGG --- ABI1
39 10 + 27057755 27057755 T C ABI1
40 10 + 61548855 61548855 G - CCDC6
41 10 + 61549659 61549659 T - CCDC6
42 10 + 61549818 61549818 A G CCDC6
43 10 + 61550057 61550057 C T CCDC6
44 10 + 61551428 61551428 T C CCDC6
45 10 + 61552692 61552692 G T CCDC6
46 10 + 61552774 61552774 C T CCDC6
47 10 + 61574378 61574379 AC -- CCDC6
48 10 + 61574381 61574381 -- CA CCDC6
49 10 + 70405855 70405855 A G TET1
50 10 + 70452471 70452471 C T TET1
51 10 + 102897057 102897057 C T TLX1
52 10 + 102897193 102897193 T C TLX1
53 10 + 102897311 102897311 A G TLX1
54 11 + 3723781 3723781 G C NUP98
55 11 + 3723941 3723941 C T NUP98
56 11 + 3733307 3733307 T C NUP98
57 11 + 3733899 3733899 C T NUP98
58 11 + 3800096 3800096 C T NUP98
59 1 + 11847691 11847691 C T MTHFR
60 1 + 11847772 11847772 G T MTHFR
61 1 + 11847861 11847861 G A MTHFR
62 1 + 11847902 11847902 C A MTHFR
63 1 + 11852300 11852300 C T MTHFR
64 1 + 11854476 11854476 T G MTHFR
65 1 + 11854896 11854896 G A MTHFR
66 1 + 11863057 11863057 G A MTHFR
67 1 + 11863904 11863904 C T MTHFR
68 1 + 11865542 11865542 A C MTHFR
69 1 + 16256076 16256076 A G SPEN
70 1 + 186275564 186275564 C T PRG4
71 1 + 186281400 186281400 C T PRG4
72 10 + 21827796 21827796 G A MLLT10
73 10 + 21962740 21962740 G A MLLT10
74 10 + 27036912 27036912 ----- GCTTT ABI1
75 10 + 61574379 61574380 CA -- CCDC6
76 10 + 70332066 70332066 C T TET1
77 10 + 70332580 70332580 A G TET1
78 10 + 102896801 102896801 G A TLX1
79 10 + 102897087 102897087 C T TLX1
80 11 + 3733434 3733435 TG -- NUP98
81 11 + 3746465 3746465 C G NUP98
82 11 + 32409472 32409472 T A WT1
83 11 + 32410002 32410002 T C WT1
84 11 + 32410337 32410337 C G WT1
85 11 + 32417945 32417945 T C WT1
86 11 + 32439038 32439038 T C WT1
87 11 + 47376448 47376448 G A SPI1
88 11 + 47380061 47380061 A C SPI1
89 11 + 47380292 47380292 -- AC SPI1
90 11 + 47380340 47380340 G T SPI1
91 11 + 69466115 69466115 C A CCND1
92 1 + 43819949 43819949 G A MPL
93 1 + 98185700 98185700 T C DPYD
94 1 + 98185712 98185713 TC -- DPYD
95 1 + 98185720 98185721 TC -- DPYD
96 1 + 98185722 98185723 AC -- DPYD
97 1 + 186277989 186277989 A G PRG4
98 1 + 186283422 186283422 C T TPR
99 10 + 27036913 27036913 ----- CTTTT ABI1
100 10 + 70405127 70405127 A G TET1
101 10 + 102890421 102890421 G A TLX1NB
102 10 + 102897305 102897305 C T TLX1
103 11 + 47379843 47379844 AT -- SPI1
104 11 + 69462910 69462910 G A CCND1
105 11 + 69466737 69466737 C G CCND1
106 11 + 85692181 85692181 A C PICALM
107 11 + 85718641 85718641 T C PICALM
108 11 + 85718663 85718663 A C PICALM
109 11 + 85725937 85725937 C T PICALM
110 11 + 108093833 108093833 G A ATM
111 11 + 108129657 108129657 A G ATM
knownSNP
1 rs4846048
2 rs4845884
3 rs70983598
4 rs3737966
5 rs2077360
6 rs868014
7 rs4846049
8 rs4846051
9 rs1994798
10 rs1801133
11 rs12063905
12 rs848208
13 rs848209
14 rs848210
15 rs848211
16 rs61749277
17
18 rs7664
19 rs977747
20 rs927462
21 rs72515113,rs56033046
22 rs2758735
23 rs291593
24 rs291592
25 rs56160474
26 rs1801159
27 rs2151562
28 rs61786598,rs61786599
29 rs1333718
30 rs1801265
31 rs14804
32 rs1538488
33 rs1293987
34 rs2273779
35 rs16825150
36 rs68069719
37 rs60597617,rs17128562,rs9285
38
39
40 rs71006293
41 rs59769275
42 rs11540401
43 rs3802695
44 rs10821594
45 rs1053266
46 rs1053265
47
48
49 rs3998860
50 rs5030882
51 rs1051723
52
53 rs1051725
54 rs35404087
55 rs35488940
56
57 rs35803045
58 rs61896892
59
60 rs3820192
61 rs1537516
62 rs1537515
63 rs1476413
64 rs1801131
65 rs2066462
66 rs2066470
67 rs3753588
68 rs3753582
69
70 rs12128607
71 rs12134934
72 rs1802669
73
74 rs60597617,rs17128562,rs9285
75
76 rs3814177
77 rs10823229
78 rs2235128
79 rs2742038
80 rs36088476
81 rs276901
82 rs5030328
83 rs5030320
84 rs5030317
85 rs16754
86 rs2295081
87 rs1057233
88 rs10734557
89 rs3832728
90 rs3740688
91 rs7177
92
93
94
95 rs61786598
96 rs61786598,rs61786599
97 rs3737940
98 rs71707233,rs61831151
99 rs9285
100
101 rs1111350
102 rs3740499
103 rs57540026
104 rs9344,rs17852153,rs71755193
105 rs678653
106 rs694353
107 rs10792821
108 rs10751133
109 rs592297
110 rs189037
111 rs672655
> pData(mapperSetExample)
accessionNumber
N01 FZY3Q2K01
N03 FZY3Q2K01
N04 FZY3Q2K02
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and