topGene: topGene
In RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Indentify diiffentially expressed genes using rank product method
Usage
1
2
Arguments
x
the value returned by function RP,
RPadvance, RSadvance, RankProducts or RP.advance
cutoff
The pfp threshold value used to select genes
method
if cutoff is provided, the method needs to be selected to identify
genes. "pfp" uses percentage of false prediction, which is a default setting.
"pval" uses p-values which is less stringent than pfp
logged
if "TRUE", data has been logged, otherwise set it to "FALSE"
logbase
base used when taking log, used to restore the fold change.The
default value is 2, this will be ignored if logged=FALSE
gene.names
if "NULL", no gene name will be attached to the output table
num.gene
number of candidates genes of interests, if cutoff is provided,
this will be ignored
Value
Two tables of identified genes with gene.index: index of gene in the original
data set RP/Rsum: Computed rank product/sum for each gene FC:(class1/class2):
Expression Fold change of class 1/ class 2. pfp: estimated pfp for each gene
if the gene is used as cutoff point P.value: estimated p-value for each gene
Table 1 list genes that are up-regulated under class 2, Table 1 ist genes that
are down-regulated under class 2
Author(s)
Fangxin Hong fhong@salk.edu
References
Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A
simple, yet powerful, new method to detect differentially regulated genes in
replicated microarray experiments, FEBS Letter, 57383-92
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
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18
19
20
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28
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30
# Load the data of Golub et al. (1999). data(golub)
# contains a 3051x38 gene expression
# matrix called golub, a vector of length called golub.cl
# that consists of the 38 class labels,
# and a matrix called golub.gnames whose third column
# contains the gene names.
data(golub)
#use a subset of data as example, apply the rank
#product method
subset <- c(1:4,28:30)
#Setting rand=123, to make the results reproducible,
#identify genes
RP.out <- RP(golub[,subset],golub.cl[subset],rand=123)
#get two lists of differentially expressed genes
#by setting FDR (false discivery rate) =0.05
table=topGene(RP.out,cutoff=0.05,method="pfp",logged=TRUE,logbase=2,
gene.names=golub.gnames[,3])
table$Table1
table$Table2
#using pvalue<0.05
topGene(RP.out,cutoff=0.05,method="pval",logged=TRUE,logbase=2,
gene.names=golub.gnames[,3])
#by selecting top 10 genes
topGene(RP.out,num.gene=10,gene.names=golub.gnames[,3])
Example output
Loading required package: Rmpfr
Loading required package: gmp
Attaching package: 'gmp'
The following objects are masked from 'package:base':
%*%, apply, crossprod, matrix, tcrossprod
C code of R package 'Rmpfr': GMP using 64 bits per limb
Attaching package: 'Rmpfr'
The following objects are masked from 'package:stats':
dbinom, dnorm, dpois, pnorm
The following objects are masked from 'package:base':
cbind, pmax, pmin, rbind
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
HG2724-HT2820_at 418 8.143 0.2689 0.05659 0.0001132
D87116_at 346 8.320 0.2605 0.03057 0.0001223
HG3494-HT3688_at 436 8.653 0.2369 0.02345 0.0001407
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
$Table1
gene.index RP/Rsum FC:(class1/class2) pfp
HG2724-HT2820_at 418 8.143 0.2689 0.05659
D87116_at 346 8.320 0.2605 0.03057
HG3494-HT3688_at 436 8.653 0.2369 0.02345
D88422_at 378 12.810 0.2684 0.06752
HG987-HT987_at 475 13.740 0.3031 0.06802
D87433_at 350 18.810 0.3543 0.15400
D26579_at 141 28.470 0.3970 0.45540
D10495_at 68 29.680 0.4748 0.44870
D26308_at 140 32.940 0.5013 0.53580
D30755_at 160 33.830 0.5308 0.51940
J03909_at 496 34.260 0.4730 0.48920
D50663_at 219 35.980 0.5953 0.51340
AFFX-HUMTFRR/M11507_3_at 13 37.430 0.5117 0.52780
D50915_at 229 38.430 0.6938 0.52660
D89052_at 381 39.490 0.4630 0.52890
HG620-HT620_at 470 42.080 0.5305 0.58710
D29643_at 155 43.170 0.5360 0.59130
AFFX-HUMTFRR/M11507_M_at 12 45.720 0.5309 0.64830
D00726_at 62 45.790 0.5530 0.61680
D83735_at 303 49.060 0.6354 0.69860
D26129_at 139 51.670 0.5489 0.75770
D79996_at 280 52.420 0.6162 0.74960
HG2788-HT2896_at 419 53.730 0.5948 0.76190
D14874_at 108 53.760 0.5693 0.73110
HG4662-HT5075_at 466 55.400 0.5835 0.75500
HG3286-HT3463_at 431 56.220 0.5563 0.75200
D87937_at 374 56.960 0.6749 0.74710
D00761_at 64 57.480 0.6040 0.73630
HG2810-HT2921_at 420 58.280 0.6070 0.73460
J03040_at 483 59.410 0.6112 0.74290
D10202_at 67 59.550 0.5783 0.72300
D86973_at 333 60.320 0.8143 0.72170
D49817_at 215 60.620 0.5280 0.70810
AF010193_at 52 60.850 0.6096 0.69310
P.value
HG2724-HT2820_at 0.0001132
D87116_at 0.0001223
HG3494-HT3688_at 0.0001407
D88422_at 0.0005401
HG987-HT987_at 0.0006802
D87433_at 0.0018470
D26579_at 0.0063750
D10495_at 0.0071790
D26308_at 0.0096450
D30755_at 0.0103900
J03909_at 0.0107600
D50663_at 0.0123200
AFFX-HUMTFRR/M11507_3_at 0.0137200
D50915_at 0.0147400
D89052_at 0.0158700
HG620-HT620_at 0.0187900
D29643_at 0.0201100
AFFX-HUMTFRR/M11507_M_at 0.0233400
D00726_at 0.0234400
D83735_at 0.0279400
D26129_at 0.0318200
D79996_at 0.0329800
HG2788-HT2896_at 0.0350500
D14874_at 0.0350900
HG4662-HT5075_at 0.0377500
HG3286-HT3463_at 0.0391000
D87937_at 0.0403500
D00761_at 0.0412300
HG2810-HT2921_at 0.0426000
J03040_at 0.0445800
D10202_at 0.0448300
D86973_at 0.0461900
D49817_at 0.0467300
AF010193_at 0.0471300
$Table2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
D88270_at 377 12.630 3.535 0.05163 5.163e-04
D11086_at 74 25.340 2.362 0.37840 4.541e-03
D50918_at 232 28.680 2.485 0.46510 6.511e-03
HG1078-HT1078_at 389 29.320 2.255 0.43330 6.933e-03
D83776_at 304 36.770 2.114 0.72640 1.308e-02
HG4036-HT4306_at 451 36.840 2.104 0.65690 1.314e-02
D86479_at 323 38.990 2.083 0.69680 1.533e-02
D86983_at 337 39.860 1.952 0.67780 1.627e-02
D87465_at 369 42.420 1.829 0.73840 1.920e-02
D83780_at 306 43.320 1.987 0.72460 2.029e-02
D42053_at 193 45.720 1.926 0.77800 2.334e-02
D30742_at 159 48.730 2.061 0.85860 2.748e-02
AFFX-HSAC07/X00351_3_st 17 50.590 1.981 0.88800 3.019e-02
D78012_at 267 51.560 1.800 0.87950 3.166e-02
D83785_at 309 54.710 1.610 0.96390 3.663e-02
HG1612-HT1612_at 394 54.850 1.853 0.92110 3.685e-02
D86970_at 330 55.590 1.897 0.90630 3.807e-02
D63880_at 259 56.580 1.753 0.90250 3.971e-02
D63486_at 248 56.750 1.891 0.86960 4.000e-02
J03600_at 491 57.810 1.610 0.87090 4.180e-02
D86967_at 329 57.900 2.127 0.83930 4.196e-02
D87076_at 344 59.890 2.068 0.87360 4.543e-02
D83783_at 307 60.980 1.714 0.87720 4.737e-02
HG3039-HT3200_at 425 61.820 1.724 0.87300 4.889e-02
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
$Table1
gene.index RP/Rsum FC:(class1/class2) pfp P.value
HG2724-HT2820_at 418 8.143 0.2689 0.05659 0.0001132
D87116_at 346 8.320 0.2605 0.03057 0.0001223
HG3494-HT3688_at 436 8.653 0.2369 0.02345 0.0001407
D88422_at 378 12.810 0.2684 0.06752 0.0005401
HG987-HT987_at 475 13.740 0.3031 0.06802 0.0006802
D87433_at 350 18.810 0.3543 0.15400 0.0018470
D26579_at 141 28.470 0.3970 0.45540 0.0063750
D10495_at 68 29.680 0.4748 0.44870 0.0071790
D26308_at 140 32.940 0.5013 0.53580 0.0096450
D30755_at 160 33.830 0.5308 0.51940 0.0103900
$Table2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
D88270_at 377 12.630 3.535 0.05163 5.163e-04
D11086_at 74 25.340 2.362 0.37840 4.541e-03
D50918_at 232 28.680 2.485 0.46510 6.511e-03
HG1078-HT1078_at 389 29.320 2.255 0.43330 6.933e-03
D83776_at 304 36.770 2.114 0.72640 1.308e-02
HG4036-HT4306_at 451 36.840 2.104 0.65690 1.314e-02
RankProd documentation built on Nov. 8, 2020, 8 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Indentify diiffentially expressed genes using rank product method
Usage
1 2 |
Arguments
x |
the value returned by function RP, RPadvance, RSadvance, RankProducts or RP.advance |
cutoff |
The pfp threshold value used to select genes |
method |
if cutoff is provided, the method needs to be selected to identify genes. "pfp" uses percentage of false prediction, which is a default setting. "pval" uses p-values which is less stringent than pfp |
logged |
if "TRUE", data has been logged, otherwise set it to "FALSE" |
logbase |
base used when taking log, used to restore the fold change.The default value is 2, this will be ignored if logged=FALSE |
gene.names |
if "NULL", no gene name will be attached to the output table |
num.gene |
number of candidates genes of interests, if cutoff is provided, this will be ignored |
Value
Two tables of identified genes with gene.index: index of gene in the original data set RP/Rsum: Computed rank product/sum for each gene FC:(class1/class2): Expression Fold change of class 1/ class 2. pfp: estimated pfp for each gene if the gene is used as cutoff point P.value: estimated p-value for each gene Table 1 list genes that are up-regulated under class 2, Table 1 ist genes that are down-regulated under class 2
Author(s)
Fangxin Hong fhong@salk.edu
References
Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments, FEBS Letter, 57383-92
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | # Load the data of Golub et al. (1999). data(golub)
# contains a 3051x38 gene expression
# matrix called golub, a vector of length called golub.cl
# that consists of the 38 class labels,
# and a matrix called golub.gnames whose third column
# contains the gene names.
data(golub)
#use a subset of data as example, apply the rank
#product method
subset <- c(1:4,28:30)
#Setting rand=123, to make the results reproducible,
#identify genes
RP.out <- RP(golub[,subset],golub.cl[subset],rand=123)
#get two lists of differentially expressed genes
#by setting FDR (false discivery rate) =0.05
table=topGene(RP.out,cutoff=0.05,method="pfp",logged=TRUE,logbase=2,
gene.names=golub.gnames[,3])
table$Table1
table$Table2
#using pvalue<0.05
topGene(RP.out,cutoff=0.05,method="pval",logged=TRUE,logbase=2,
gene.names=golub.gnames[,3])
#by selecting top 10 genes
topGene(RP.out,num.gene=10,gene.names=golub.gnames[,3])
|
Example output
Loading required package: Rmpfr
Loading required package: gmp
Attaching package: 'gmp'
The following objects are masked from 'package:base':
%*%, apply, crossprod, matrix, tcrossprod
C code of R package 'Rmpfr': GMP using 64 bits per limb
Attaching package: 'Rmpfr'
The following objects are masked from 'package:stats':
dbinom, dnorm, dpois, pnorm
The following objects are masked from 'package:base':
cbind, pmax, pmin, rbind
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
HG2724-HT2820_at 418 8.143 0.2689 0.05659 0.0001132
D87116_at 346 8.320 0.2605 0.03057 0.0001223
HG3494-HT3688_at 436 8.653 0.2369 0.02345 0.0001407
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
$Table1
gene.index RP/Rsum FC:(class1/class2) pfp
HG2724-HT2820_at 418 8.143 0.2689 0.05659
D87116_at 346 8.320 0.2605 0.03057
HG3494-HT3688_at 436 8.653 0.2369 0.02345
D88422_at 378 12.810 0.2684 0.06752
HG987-HT987_at 475 13.740 0.3031 0.06802
D87433_at 350 18.810 0.3543 0.15400
D26579_at 141 28.470 0.3970 0.45540
D10495_at 68 29.680 0.4748 0.44870
D26308_at 140 32.940 0.5013 0.53580
D30755_at 160 33.830 0.5308 0.51940
J03909_at 496 34.260 0.4730 0.48920
D50663_at 219 35.980 0.5953 0.51340
AFFX-HUMTFRR/M11507_3_at 13 37.430 0.5117 0.52780
D50915_at 229 38.430 0.6938 0.52660
D89052_at 381 39.490 0.4630 0.52890
HG620-HT620_at 470 42.080 0.5305 0.58710
D29643_at 155 43.170 0.5360 0.59130
AFFX-HUMTFRR/M11507_M_at 12 45.720 0.5309 0.64830
D00726_at 62 45.790 0.5530 0.61680
D83735_at 303 49.060 0.6354 0.69860
D26129_at 139 51.670 0.5489 0.75770
D79996_at 280 52.420 0.6162 0.74960
HG2788-HT2896_at 419 53.730 0.5948 0.76190
D14874_at 108 53.760 0.5693 0.73110
HG4662-HT5075_at 466 55.400 0.5835 0.75500
HG3286-HT3463_at 431 56.220 0.5563 0.75200
D87937_at 374 56.960 0.6749 0.74710
D00761_at 64 57.480 0.6040 0.73630
HG2810-HT2921_at 420 58.280 0.6070 0.73460
J03040_at 483 59.410 0.6112 0.74290
D10202_at 67 59.550 0.5783 0.72300
D86973_at 333 60.320 0.8143 0.72170
D49817_at 215 60.620 0.5280 0.70810
AF010193_at 52 60.850 0.6096 0.69310
P.value
HG2724-HT2820_at 0.0001132
D87116_at 0.0001223
HG3494-HT3688_at 0.0001407
D88422_at 0.0005401
HG987-HT987_at 0.0006802
D87433_at 0.0018470
D26579_at 0.0063750
D10495_at 0.0071790
D26308_at 0.0096450
D30755_at 0.0103900
J03909_at 0.0107600
D50663_at 0.0123200
AFFX-HUMTFRR/M11507_3_at 0.0137200
D50915_at 0.0147400
D89052_at 0.0158700
HG620-HT620_at 0.0187900
D29643_at 0.0201100
AFFX-HUMTFRR/M11507_M_at 0.0233400
D00726_at 0.0234400
D83735_at 0.0279400
D26129_at 0.0318200
D79996_at 0.0329800
HG2788-HT2896_at 0.0350500
D14874_at 0.0350900
HG4662-HT5075_at 0.0377500
HG3286-HT3463_at 0.0391000
D87937_at 0.0403500
D00761_at 0.0412300
HG2810-HT2921_at 0.0426000
J03040_at 0.0445800
D10202_at 0.0448300
D86973_at 0.0461900
D49817_at 0.0467300
AF010193_at 0.0471300
$Table2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
D88270_at 377 12.630 3.535 0.05163 5.163e-04
D11086_at 74 25.340 2.362 0.37840 4.541e-03
D50918_at 232 28.680 2.485 0.46510 6.511e-03
HG1078-HT1078_at 389 29.320 2.255 0.43330 6.933e-03
D83776_at 304 36.770 2.114 0.72640 1.308e-02
HG4036-HT4306_at 451 36.840 2.104 0.65690 1.314e-02
D86479_at 323 38.990 2.083 0.69680 1.533e-02
D86983_at 337 39.860 1.952 0.67780 1.627e-02
D87465_at 369 42.420 1.829 0.73840 1.920e-02
D83780_at 306 43.320 1.987 0.72460 2.029e-02
D42053_at 193 45.720 1.926 0.77800 2.334e-02
D30742_at 159 48.730 2.061 0.85860 2.748e-02
AFFX-HSAC07/X00351_3_st 17 50.590 1.981 0.88800 3.019e-02
D78012_at 267 51.560 1.800 0.87950 3.166e-02
D83785_at 309 54.710 1.610 0.96390 3.663e-02
HG1612-HT1612_at 394 54.850 1.853 0.92110 3.685e-02
D86970_at 330 55.590 1.897 0.90630 3.807e-02
D63880_at 259 56.580 1.753 0.90250 3.971e-02
D63486_at 248 56.750 1.891 0.86960 4.000e-02
J03600_at 491 57.810 1.610 0.87090 4.180e-02
D86967_at 329 57.900 2.127 0.83930 4.196e-02
D87076_at 344 59.890 2.068 0.87360 4.543e-02
D83783_at 307 60.980 1.714 0.87720 4.737e-02
HG3039-HT3200_at 425 61.820 1.724 0.87300 4.889e-02
Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
$Table1
gene.index RP/Rsum FC:(class1/class2) pfp P.value
HG2724-HT2820_at 418 8.143 0.2689 0.05659 0.0001132
D87116_at 346 8.320 0.2605 0.03057 0.0001223
HG3494-HT3688_at 436 8.653 0.2369 0.02345 0.0001407
D88422_at 378 12.810 0.2684 0.06752 0.0005401
HG987-HT987_at 475 13.740 0.3031 0.06802 0.0006802
D87433_at 350 18.810 0.3543 0.15400 0.0018470
D26579_at 141 28.470 0.3970 0.45540 0.0063750
D10495_at 68 29.680 0.4748 0.44870 0.0071790
D26308_at 140 32.940 0.5013 0.53580 0.0096450
D30755_at 160 33.830 0.5308 0.51940 0.0103900
$Table2
gene.index RP/Rsum FC:(class1/class2) pfp P.value
AFFX-HUMRGE/M10098_3_at 6 6.768 4.314 0.02786 5.573e-05
AFFX-HUMRGE/M10098_M_at 5 9.967 3.849 0.05780 2.312e-04
AFFX-HUMRGE/M10098_5_at 4 10.780 4.034 0.05054 3.032e-04
AFFX-M27830_5_at 14 10.800 3.252 0.03811 3.049e-04
D88270_at 377 12.630 3.535 0.05163 5.163e-04
D11086_at 74 25.340 2.362 0.37840 4.541e-03
D50918_at 232 28.680 2.485 0.46510 6.511e-03
HG1078-HT1078_at 389 29.320 2.255 0.43330 6.933e-03
D83776_at 304 36.770 2.114 0.72640 1.308e-02
HG4036-HT4306_at 451 36.840 2.104 0.65690 1.314e-02
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