GetExampleData: Get the example data
In ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
Description
Usage
Arguments
Details
Author(s)
Examples
Description
Get the example data.
Usage
1
2
GetExampleData(exampleData)
Arguments
exampleData
A character string, must be one of "dataset", "class.labels" and "controlcharactor".
Details
The function GetExampleData(exampleData="dataset") obtains gene expression dataset from the environment variable envData.
The function GetExampleData(exampleData="class.labels") obtains class labels from the environment variable envData.
The function GetExampleData(exampleData="controlcharactor") obtains control sample label from the environment variable envData.
Author(s)
Junwei Han <hanjunwei1981@163.com>, Xinrui Shi<xinrui103@163.com> and Chunquan Li <lcqbio@163.com>
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
## Not run:
#obtain the gene expression dataset.
dataset<-GetExampleData(exampleData="dataset")
dataset[1:10,]
#obtain the class labels.
class.labels<-GetExampleData(exampleData="class.labels")
#obtain the control sample label.
controlcharactor<-GetExampleData(exampleData="controlcharactor")
## End(Not run)
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: XML
Loading required package: parmigene
X786.0 BT.549 CCRF.CEM COLO.205 EKVX HCC.2998 HCT.15 HOP.62 HOP.92
TACC2 46.05 82.17 16.87 98.60 141.02 114.32 134.34 44.95 73.96
C14orf132 108.34 59.04 25.61 33.11 42.53 9.12 9.36 310.96 101.74
AGER 42.20 25.75 76.01 40.41 32.17 48.28 58.27 42.40 49.68
32385_at 7.43 13.94 8.55 21.13 15.09 19.05 16.47 7.60 10.88
RBM17 11.40 3.00 3.16 2.34 4.43 1.56 6.04 6.16 1.41
DYT1 148.09 317.17 316.66 147.23 125.78 261.39 268.41 212.51 142.51
CORO1A 8.62 9.12 1572.53 5.91 5.31 11.98 128.77 7.51 7.04
WT1 206.74 136.71 141.34 129.09 138.01 138.16 130.14 123.80 131.91
SYCP2 7.94 35.68 7.80 1.97 7.75 4.73 7.23 5.72 2.02
SULF1 10.45 8.50 4.05 4.77 2.35 3.72 3.34 809.88 2.58
HS.578T HT29 K.562 KM12 M14 MDA.MB.231.ATCC MDA.MB.435
TACC2 74.29 130.04 24.04 197.63 33.82 72.22 53.78
C14orf132 241.05 15.52 19.46 5.05 32.39 18.11 18.40
AGER 58.18 59.93 36.98 45.58 32.58 48.13 45.04
32385_at 9.36 14.91 14.37 15.96 13.75 6.21 11.21
RBM17 7.10 2.05 2.85 1.43 4.92 5.45 2.60
DYT1 163.06 252.58 183.74 174.92 156.65 241.41 177.62
CORO1A 6.01 5.67 15.35 8.05 6.29 6.22 7.94
WT1 142.58 94.59 148.70 127.90 115.71 113.40 157.55
SYCP2 1.16 25.92 15.13 4.79 17.41 9.40 3.68
SULF1 1211.69 2.77 5.62 4.85 4.93 4.93 6.06
NCI.H23 NCI.H322M NCI.H522 OVCAR.3 OVCAR.5 OVCAR.8 PC.3 RXF.393
TACC2 64.19 143.13 117.26 84.13 68.02 50.28 121.26 61.71
C14orf132 122.97 55.60 476.71 8.82 118.18 61.78 13.35 201.98
AGER 47.23 34.63 50.89 81.55 32.77 78.38 31.17 54.79
32385_at 23.30 23.64 5.08 7.89 18.98 6.57 12.28 15.27
RBM17 3.05 1.55 5.30 2.32 3.70 10.68 1.70 18.46
DYT1 145.95 153.50 197.27 180.19 95.37 144.08 180.56 139.77
CORO1A 9.81 18.60 17.42 11.92 6.70 11.52 6.99 8.30
WT1 140.15 114.75 136.16 194.27 119.22 159.28 162.04 139.33
SYCP2 20.36 20.94 49.65 15.37 16.36 22.80 3.83 5.63
SULF1 4.06 7.77 5.02 9.80 5.40 3.59 5.27 4.19
SF.268 SF.295 SK.MEL.2 SN12C SNB.19 SNB.75 SW.620 T.47D U251
TACC2 59.32 53.55 25.63 49.38 41.69 36.40 115.17 77.26 54.01
C14orf132 365.86 90.39 17.65 36.07 73.15 99.03 65.20 276.99 64.28
AGER 58.89 44.37 33.59 55.23 67.11 58.36 45.53 57.24 57.92
32385_at 11.16 9.63 12.49 13.05 22.40 10.82 22.45 11.04 27.87
RBM17 2.89 1.97 5.66 6.06 6.09 4.50 2.33 2.60 2.43
DYT1 208.89 239.60 184.68 104.51 156.87 292.95 188.76 240.81 176.09
CORO1A 7.71 8.44 8.72 10.06 12.34 9.94 9.21 8.04 10.00
WT1 137.79 124.98 150.76 155.60 164.30 137.36 128.35 146.42 125.39
SYCP2 5.59 7.31 17.86 12.87 3.54 6.62 4.58 189.97 1.73
SULF1 13.44 3.16 7.61 5.00 4.90 192.55 3.81 161.56 3.74
A498 A549.ATCC ACHN CAKI.1 HCT.116 LOX.IMVI MALME.3M MCF7
TACC2 58.13 292.17 49.30 68.55 101.68 66.25 60.43 68.14
C14orf132 43.73 78.34 15.70 11.62 62.60 11.26 260.59 159.32
AGER 48.52 52.24 55.27 54.84 24.68 57.29 49.69 51.50
32385_at 16.71 4.51 16.63 8.17 3.59 8.04 8.36 30.77
RBM17 6.64 3.28 3.00 3.43 4.50 3.49 6.39 1.62
DYT1 267.59 219.67 203.68 183.59 192.54 135.79 163.07 236.47
CORO1A 14.18 7.29 8.28 9.05 7.69 6.13 10.07 6.16
WT1 179.79 148.33 132.79 144.91 119.88 135.98 148.20 108.32
SYCP2 9.62 14.02 17.40 7.14 5.01 6.22 6.83 15.27
SULF1 6.66 5.69 3.99 6.04 3.59 5.14 5.20 15.30
MOLT.4 NCI.H460 OVCAR.4 SF.539 SK.MEL.5 SR UACC.257 UACC.62
TACC2 32.21 105.89 64.99 53.52 85.47 18.69 32.16 45.70
C14orf132 10.71 13.59 53.78 57.57 86.80 17.30 102.66 62.16
AGER 61.48 44.44 45.68 54.17 62.53 83.18 56.57 50.40
32385_at 21.27 13.36 16.19 12.07 17.62 22.60 4.50 14.59
RBM17 2.77 4.42 8.91 12.28 3.04 10.13 8.32 8.23
DYT1 343.63 242.40 140.25 249.77 76.10 192.20 120.47 122.92
CORO1A 1344.20 8.01 9.02 8.05 13.44 452.16 8.62 12.12
WT1 187.81 116.87 168.60 125.96 217.17 153.87 175.60 230.56
SYCP2 120.72 12.74 3.64 8.89 7.18 3.49 7.53 4.36
SULF1 6.71 5.53 6.05 5.10 4.00 4.21 5.22 10.01
UO.31
TACC2 48.13
C14orf132 73.44
AGER 36.75
32385_at 11.33
RBM17 3.91
DYT1 230.18
CORO1A 7.76
WT1 139.53
SYCP2 13.36
SULF1 8.59
ESEA documentation built on May 2, 2019, 3:41 p.m.
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Description Usage Arguments Details Author(s) Examples
Description
Get the example data.
Usage
1 2 | GetExampleData(exampleData)
|
Arguments
exampleData |
A character string, must be one of "dataset", "class.labels" and "controlcharactor". |
Details
The function GetExampleData(exampleData="dataset") obtains gene expression dataset from the environment variable envData.
The function GetExampleData(exampleData="class.labels") obtains class labels from the environment variable envData.
The function GetExampleData(exampleData="controlcharactor") obtains control sample label from the environment variable envData.
Author(s)
Junwei Han <hanjunwei1981@163.com>, Xinrui Shi<xinrui103@163.com> and Chunquan Li <lcqbio@163.com>
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## Not run:
#obtain the gene expression dataset.
dataset<-GetExampleData(exampleData="dataset")
dataset[1:10,]
#obtain the class labels.
class.labels<-GetExampleData(exampleData="class.labels")
#obtain the control sample label.
controlcharactor<-GetExampleData(exampleData="controlcharactor")
## End(Not run)
|
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: XML
Loading required package: parmigene
X786.0 BT.549 CCRF.CEM COLO.205 EKVX HCC.2998 HCT.15 HOP.62 HOP.92
TACC2 46.05 82.17 16.87 98.60 141.02 114.32 134.34 44.95 73.96
C14orf132 108.34 59.04 25.61 33.11 42.53 9.12 9.36 310.96 101.74
AGER 42.20 25.75 76.01 40.41 32.17 48.28 58.27 42.40 49.68
32385_at 7.43 13.94 8.55 21.13 15.09 19.05 16.47 7.60 10.88
RBM17 11.40 3.00 3.16 2.34 4.43 1.56 6.04 6.16 1.41
DYT1 148.09 317.17 316.66 147.23 125.78 261.39 268.41 212.51 142.51
CORO1A 8.62 9.12 1572.53 5.91 5.31 11.98 128.77 7.51 7.04
WT1 206.74 136.71 141.34 129.09 138.01 138.16 130.14 123.80 131.91
SYCP2 7.94 35.68 7.80 1.97 7.75 4.73 7.23 5.72 2.02
SULF1 10.45 8.50 4.05 4.77 2.35 3.72 3.34 809.88 2.58
HS.578T HT29 K.562 KM12 M14 MDA.MB.231.ATCC MDA.MB.435
TACC2 74.29 130.04 24.04 197.63 33.82 72.22 53.78
C14orf132 241.05 15.52 19.46 5.05 32.39 18.11 18.40
AGER 58.18 59.93 36.98 45.58 32.58 48.13 45.04
32385_at 9.36 14.91 14.37 15.96 13.75 6.21 11.21
RBM17 7.10 2.05 2.85 1.43 4.92 5.45 2.60
DYT1 163.06 252.58 183.74 174.92 156.65 241.41 177.62
CORO1A 6.01 5.67 15.35 8.05 6.29 6.22 7.94
WT1 142.58 94.59 148.70 127.90 115.71 113.40 157.55
SYCP2 1.16 25.92 15.13 4.79 17.41 9.40 3.68
SULF1 1211.69 2.77 5.62 4.85 4.93 4.93 6.06
NCI.H23 NCI.H322M NCI.H522 OVCAR.3 OVCAR.5 OVCAR.8 PC.3 RXF.393
TACC2 64.19 143.13 117.26 84.13 68.02 50.28 121.26 61.71
C14orf132 122.97 55.60 476.71 8.82 118.18 61.78 13.35 201.98
AGER 47.23 34.63 50.89 81.55 32.77 78.38 31.17 54.79
32385_at 23.30 23.64 5.08 7.89 18.98 6.57 12.28 15.27
RBM17 3.05 1.55 5.30 2.32 3.70 10.68 1.70 18.46
DYT1 145.95 153.50 197.27 180.19 95.37 144.08 180.56 139.77
CORO1A 9.81 18.60 17.42 11.92 6.70 11.52 6.99 8.30
WT1 140.15 114.75 136.16 194.27 119.22 159.28 162.04 139.33
SYCP2 20.36 20.94 49.65 15.37 16.36 22.80 3.83 5.63
SULF1 4.06 7.77 5.02 9.80 5.40 3.59 5.27 4.19
SF.268 SF.295 SK.MEL.2 SN12C SNB.19 SNB.75 SW.620 T.47D U251
TACC2 59.32 53.55 25.63 49.38 41.69 36.40 115.17 77.26 54.01
C14orf132 365.86 90.39 17.65 36.07 73.15 99.03 65.20 276.99 64.28
AGER 58.89 44.37 33.59 55.23 67.11 58.36 45.53 57.24 57.92
32385_at 11.16 9.63 12.49 13.05 22.40 10.82 22.45 11.04 27.87
RBM17 2.89 1.97 5.66 6.06 6.09 4.50 2.33 2.60 2.43
DYT1 208.89 239.60 184.68 104.51 156.87 292.95 188.76 240.81 176.09
CORO1A 7.71 8.44 8.72 10.06 12.34 9.94 9.21 8.04 10.00
WT1 137.79 124.98 150.76 155.60 164.30 137.36 128.35 146.42 125.39
SYCP2 5.59 7.31 17.86 12.87 3.54 6.62 4.58 189.97 1.73
SULF1 13.44 3.16 7.61 5.00 4.90 192.55 3.81 161.56 3.74
A498 A549.ATCC ACHN CAKI.1 HCT.116 LOX.IMVI MALME.3M MCF7
TACC2 58.13 292.17 49.30 68.55 101.68 66.25 60.43 68.14
C14orf132 43.73 78.34 15.70 11.62 62.60 11.26 260.59 159.32
AGER 48.52 52.24 55.27 54.84 24.68 57.29 49.69 51.50
32385_at 16.71 4.51 16.63 8.17 3.59 8.04 8.36 30.77
RBM17 6.64 3.28 3.00 3.43 4.50 3.49 6.39 1.62
DYT1 267.59 219.67 203.68 183.59 192.54 135.79 163.07 236.47
CORO1A 14.18 7.29 8.28 9.05 7.69 6.13 10.07 6.16
WT1 179.79 148.33 132.79 144.91 119.88 135.98 148.20 108.32
SYCP2 9.62 14.02 17.40 7.14 5.01 6.22 6.83 15.27
SULF1 6.66 5.69 3.99 6.04 3.59 5.14 5.20 15.30
MOLT.4 NCI.H460 OVCAR.4 SF.539 SK.MEL.5 SR UACC.257 UACC.62
TACC2 32.21 105.89 64.99 53.52 85.47 18.69 32.16 45.70
C14orf132 10.71 13.59 53.78 57.57 86.80 17.30 102.66 62.16
AGER 61.48 44.44 45.68 54.17 62.53 83.18 56.57 50.40
32385_at 21.27 13.36 16.19 12.07 17.62 22.60 4.50 14.59
RBM17 2.77 4.42 8.91 12.28 3.04 10.13 8.32 8.23
DYT1 343.63 242.40 140.25 249.77 76.10 192.20 120.47 122.92
CORO1A 1344.20 8.01 9.02 8.05 13.44 452.16 8.62 12.12
WT1 187.81 116.87 168.60 125.96 217.17 153.87 175.60 230.56
SYCP2 120.72 12.74 3.64 8.89 7.18 3.49 7.53 4.36
SULF1 6.71 5.53 6.05 5.10 4.00 4.21 5.22 10.01
UO.31
TACC2 48.13
C14orf132 73.44
AGER 36.75
32385_at 11.33
RBM17 3.91
DYT1 230.18
CORO1A 7.76
WT1 139.53
SYCP2 13.36
SULF1 8.59
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