yeast: Saccharomyces Cerevisiae eQTL data from Kruglak et. al....
In geneNetBP: Belief Propagation in Genotype-Phenotype Networks
Description
Usage
Format
Details
Source
Examples
Description
eQTL data from 112 F1 segregants from a cross between BY4716 and RM11-1a strains of Saccharomyces Cerevisiae.
Usage
1
Format
The data set yeast is a data frame of 112 observations of 50 variables: genotype data (genotype states at 12 SNP markers) and phenotype data (normalized and discretized expression values of 38 genes). Both genotypes and phenotypes are of class factor.
Details
The yeast dataset is a subset of the widely studied yeast expression dataset comprising of 112 F1 segregants from a cross between BY4716 and RM11-1a strains of Saccharomyces Cerevisiae. The original dataset consists of expression values reported as log2(sample/ BY reference) for 6216 genes. The data can be accessed in Gene Expression Omnibus (GEO) by accession number (GSE1990). After linkage analysis and filtering based on location and significance of QTL, a final set of 38 genes and their corresponding 12 SNP markers were identified and included in the yeast dataset. The gene expression values are discretized around the median and have two states, 1 (above or equal to median) and -1 (below median). There are two genotype states: 1 or 2.\
Thus the final dataset is a data frame of 112 observations (genotype) of 12 variables (SNP markers) and normalized gene expression of 38 variables (genes).\
Source
Brem RB, Kruglyak L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 2005 Feb 1;102(5):1572-7.\
Brem RB, Storey JD, Whittle J, Kruglyak L. Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 2005 Aug 4;436(7051):701-3.\
Examples
1
2
3
4
5
6
Example output
Loading required package: Rgraphviz
Loading required package: graph
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: grid
Loading required package: bnlearn
Attaching package: 'bnlearn'
The following object is masked from 'package:BiocGenerics':
score
The following object is masked from 'package:stats':
sigma
Loading required package: gRain
Loading required package: gRbase
Attaching package: 'gRbase'
The following objects are masked from 'package:bnlearn':
ancestors, children, parents
$dbn
Bayesian network parameters
Parameters of node HEM3 (multinomial distribution)
Conditional probability table:
, , Qchr4 = 1
YNL045W
HEM3 -1 1
-1 0.8695652 1.0000000
1 0.1304348 0.0000000
, , Qchr4 = 2
YNL045W
HEM3 -1 1
-1 0.0000000 0.1304348
1 1.0000000 0.8695652
Parameters of node BAP2 (multinomial distribution)
Conditional probability table:
, , Qchr2 = 1
Qchr3
BAP2 1 2
-1 0.00000000 0.80645161
1 1.00000000 0.19354839
, , Qchr2 = 2
Qchr3
BAP2 1 2
-1 0.15789474 0.96551724
1 0.84210526 0.03448276
Parameters of node ERG9 (multinomial distribution)
Conditional probability table:
Qchr12
ERG9 1 2
-1 0.07843137 0.85245902
1 0.92156863 0.14754098
Parameters of node PHA2 (multinomial distribution)
Conditional probability table:
, , MSY1 = -1, Qchr14 = 1
BAP2
PHA2 -1 1
-1 0.4375000 0.0000000
1 0.5625000 1.0000000
, , MSY1 = 1, Qchr14 = 1
BAP2
PHA2 -1 1
-1 0.0000000 0.0000000
1 1.0000000 1.0000000
, , MSY1 = -1, Qchr14 = 2
BAP2
PHA2 -1 1
-1 0.8571429 1.0000000
1 0.1428571 0.0000000
, , MSY1 = 1, Qchr14 = 2
BAP2
PHA2 -1 1
-1 1.0000000 0.6000000
1 0.0000000 0.4000000
Parameters of node ERG6 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1
LCB4
ERG6 -1 1
-1 0.0000000 0.1351351
1 1.0000000 0.8648649
, , Qchr12 = 2
LCB4
ERG6 -1 1
-1 0.7619048 1.0000000
1 0.2380952 0.0000000
Parameters of node ERG12 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1
YEL047C
ERG12 -1 1
-1 0.2903226 0.0000000
1 0.7096774 1.0000000
, , Qchr12 = 2
YEL047C
ERG12 -1 1
-1 0.8400000 0.7222222
1 0.1600000 0.2777778
Parameters of node TAT1 (multinomial distribution)
Conditional probability table:
, , Qchr5 = 1
Qchr2
TAT1 1 2
-1 0.91489362 0.20000000
1 0.08510638 0.80000000
, , Qchr5 = 2
Qchr2
TAT1 1 2
-1 0.41176471 0.00000000
1 0.58823529 1.00000000
Parameters of node FLX1 (multinomial distribution)
Conditional probability table:
, , Qchr9 = 1
MSE1
FLX1 -1 1
-1 1.0000000 0.5909091
1 0.0000000 0.4090909
, , Qchr9 = 2
MSE1
FLX1 -1 1
-1 0.2800000 0.1470588
1 0.7200000 0.8529412
Parameters of node MSY1 (multinomial distribution)
Conditional probability table:
GRX5
MSY1 -1 1
-1 0.6428571 0.3571429
1 0.3571429 0.6428571
Parameters of node GRX5 (multinomial distribution)
Conditional probability table:
, , Qchr16 = 1
YAT2
GRX5 -1 1
-1 0.7105263 0.9047619
1 0.2894737 0.0952381
, , Qchr16 = 2
YAT2
GRX5 -1 1
-1 0.0000000 0.2857143
1 1.0000000 0.7142857
Parameters of node VMA13 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
YNL045W
VMA13 -1 1
-1 0.4117647 0.2051282
1 0.5882353 0.7948718
, , COX10 = 1
YNL045W
VMA13 -1 1
-1 0.8717949 0.4117647
1 0.1282051 0.5882353
Parameters of node LAT1 (multinomial distribution)
Conditional probability table:
YNL045W
LAT1 -1 1
-1 0.6785714 0.3214286
1 0.3214286 0.6785714
Parameters of node NCP1 (multinomial distribution)
Conditional probability table:
, , Qchr8 = 1
MSY1
NCP1 -1 1
-1 0.6571429 0.7575758
1 0.3428571 0.2424242
, , Qchr8 = 2
MSY1
NCP1 -1 1
-1 0.0000000 0.3478261
1 1.0000000 0.6521739
Parameters of node SLM5 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
YAT2
SLM5 -1 1
-1 0.7391304 1.0000000
1 0.2608696 0.0000000
, , COX10 = 1
YAT2
SLM5 -1 1
-1 0.1818182 0.0000000
1 0.8181818 1.0000000
Parameters of node MSE1 (multinomial distribution)
Conditional probability table:
, , MSK1 = -1
DIA4
MSE1 -1 1
-1 0.95238095 0.42857143
1 0.04761905 0.57142857
, , MSK1 = 1
DIA4
MSE1 -1 1
-1 0.28571429 0.14285714
1 0.71428571 0.85714286
Parameters of node ALD6 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1, Qchr13 = 1
Qchr3
ALD6 1 2
-1 0.27272727 0.07142857
1 0.72727273 0.92857143
, , Qchr12 = 2, Qchr13 = 1
Qchr3
ALD6 1 2
-1 0.83333333 0.11111111
1 0.16666667 0.88888889
, , Qchr12 = 1, Qchr13 = 2
Qchr3
ALD6 1 2
-1 0.41666667 0.57142857
1 0.58333333 0.42857143
, , Qchr12 = 2, Qchr13 = 2
Qchr3
ALD6 1 2
-1 1.00000000 0.71428571
1 0.00000000 0.28571429
Parameters of node HIS3 (multinomial distribution)
Conditional probability table:
, , Qchr13 = 1
BAP2
HIS3 -1 1
-1 0.9062500 0.1304348
1 0.0937500 0.8695652
, , Qchr13 = 2
BAP2
HIS3 -1 1
-1 0.5833333 0.3030303
1 0.4166667 0.6969697
Parameters of node NAM2 (multinomial distribution)
Conditional probability table:
, , TYS1 = -1
MSY1
NAM2 -1 1
-1 0.68421053 0.08108108
1 0.31578947 0.91891892
, , TYS1 = 1
MSY1
NAM2 -1 1
-1 0.91891892 0.31578947
1 0.08108108 0.68421053
Parameters of node ACS1 (multinomial distribution)
Conditional probability table:
, , Qchr1 = 1
TYS1
ACS1 -1 1
-1 0.44827586 0.96296296
1 0.55172414 0.03703704
, , Qchr1 = 2
TYS1
ACS1 -1 1
-1 0.22222222 0.37931034
1 0.77777778 0.62068966
Parameters of node YNL045W (multinomial distribution)
Conditional probability table:
, , ACS1 = -1, RBK1 = -1
SLM5
YNL045W -1 1
-1 0.91666667 1.00000000
1 0.08333333 0.00000000
, , ACS1 = 1, RBK1 = -1
SLM5
YNL045W -1 1
-1 0.00000000 0.63636364
1 1.00000000 0.36363636
, , ACS1 = -1, RBK1 = 1
SLM5
YNL045W -1 1
-1 0.47619048 0.00000000
1 0.52380952 1.00000000
, , ACS1 = 1, RBK1 = 1
SLM5
YNL045W -1 1
-1 0.00000000 0.27272727
1 1.00000000 0.72727273
Parameters of node RBK1 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
MSY1
RBK1 -1 1
-1 0.2352941 0.0000000
1 0.7647059 1.0000000
, , COX10 = 1
MSY1
RBK1 -1 1
-1 0.2000000 0.8431373
1 0.8000000 0.1568627
Parameters of node YMR293C (multinomial distribution)
Conditional probability table:
COX10
YMR293C -1 1
-1 0.8928571 0.1071429
1 0.1071429 0.8928571
Parameters of node LCB4 (multinomial distribution)
Conditional probability table:
, , Qchr2 = 1
Qchr12
LCB4 1 2
-1 0.06451613 0.51515152
1 0.93548387 0.48484848
, , Qchr2 = 2
Qchr12
LCB4 1 2
-1 0.60000000 0.89285714
1 0.40000000 0.10714286
Parameters of node PPA2 (multinomial distribution)
Conditional probability table:
, , YAT2 = -1
MSY1
PPA2 -1 1
-1 0.64000000 0.12903226
1 0.36000000 0.87096774
, , YAT2 = 1
MSY1
PPA2 -1 1
-1 0.96774194 0.24000000
1 0.03225806 0.76000000
Parameters of node DIA4 (multinomial distribution)
Conditional probability table:
SLM5
DIA4 -1 1
-1 0.8392857 0.1607143
1 0.1607143 0.8392857
Parameters of node MIR1 (multinomial distribution)
Conditional probability table:
, , Qchr15 = 1
PPA2
MIR1 -1 1
-1 0.4761905 0.1562500
1 0.5238095 0.8437500
, , Qchr15 = 2
PPA2
MIR1 -1 1
-1 0.8857143 0.4166667
1 0.1142857 0.5833333
Parameters of node YEL047C (multinomial distribution)
Conditional probability table:
MSY1
YEL047C -1 1
-1 0.3214286 0.6785714
1 0.6785714 0.3214286
Parameters of node MSK1 (multinomial distribution)
Conditional probability table:
MSY1
MSK1 -1 1
-1 0.875 0.125
1 0.125 0.875
Parameters of node TRP3 (multinomial distribution)
Conditional probability table:
HIS3
TRP3 -1 1
-1 0.7857143 0.2142857
1 0.2142857 0.7857143
Parameters of node THI22 (multinomial distribution)
Conditional probability table:
LCB4
THI22 -1 1
-1 0.3392857 0.6607143
1 0.6607143 0.3392857
Parameters of node TNA1 (multinomial distribution)
Conditional probability table:
, , RBK1 = -1
ACS1
TNA1 -1 1
-1 0.6333333 0.1153846
1 0.3666667 0.8846154
, , RBK1 = 1
ACS1
TNA1 -1 1
-1 0.7692308 0.4666667
1 0.2307692 0.5333333
Parameters of node MSD1 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
MSK1
MSD1 -1 1
-1 0.93617021 0.22222222
1 0.06382979 0.77777778
, , COX10 = 1
MSK1
MSD1 -1 1
-1 0.44444444 0.12765957
1 0.55555556 0.87234043
Parameters of node YER152C (multinomial distribution)
Conditional probability table:
, , Qchr4 = 1
NCP1
YER152C -1 1
-1 0.8064516 0.4800000
1 0.1935484 0.5200000
, , Qchr4 = 2
NCP1
YER152C -1 1
-1 0.6000000 0.1290323
1 0.4000000 0.8709677
Parameters of node TAT2 (multinomial distribution)
Conditional probability table:
NAM2
TAT2 -1 1
-1 0.6964286 0.3035714
1 0.3035714 0.6964286
Parameters of node TYS1 (multinomial distribution)
Conditional probability table:
, , TRP3 = -1
PPA2
TYS1 -1 1
-1 0.5000000 0.8529412
1 0.5000000 0.1470588
, , TRP3 = 1
PPA2
TYS1 -1 1
-1 0.1176471 0.5454545
1 0.8823529 0.4545455
Parameters of node YAT2 (multinomial distribution)
Conditional probability table:
HIS3
YAT2 -1 1
-1 0.75 0.25
1 0.25 0.75
Parameters of node YEL041W (multinomial distribution)
Conditional probability table:
-1 1
0.5 0.5
Parameters of node COX10 (multinomial distribution)
Conditional probability table:
, , TAT2 = -1
MSY1
COX10 -1 1
-1 0.91891892 0.26315789
1 0.08108108 0.73684211
, , TAT2 = 1
MSY1
COX10 -1 1
-1 0.89473684 0.00000000
1 0.10526316 1.00000000
Parameters of node Qchr4 (multinomial distribution)
Conditional probability table:
1 2
0.5 0.5
Parameters of node Qchr3 (multinomial distribution)
Conditional probability table:
1 2
0.4642857 0.5357143
Parameters of node Qchr12 (multinomial distribution)
Conditional probability table:
1 2
0.4553571 0.5446429
Parameters of node Qchr14 (multinomial distribution)
Conditional probability table:
1 2
0.4910714 0.5089286
Parameters of node Qchr2 (multinomial distribution)
Conditional probability table:
1 2
0.5714286 0.4285714
Parameters of node Qchr5 (multinomial distribution)
Conditional probability table:
1 2
0.6875 0.3125
Parameters of node Qchr9 (multinomial distribution)
Conditional probability table:
1 2
0.4732143 0.5267857
Parameters of node Qchr16 (multinomial distribution)
Conditional probability table:
1 2
0.5267857 0.4732143
Parameters of node Qchr8 (multinomial distribution)
Conditional probability table:
1 2
0.6071429 0.3928571
Parameters of node Qchr13 (multinomial distribution)
Conditional probability table:
1 2
0.4910714 0.5089286
Parameters of node Qchr1 (multinomial distribution)
Conditional probability table:
1 2
0.5 0.5
Parameters of node Qchr15 (multinomial distribution)
Conditional probability table:
1 2
0.4732143 0.5267857
$marginal
$marginal$pheno
$marginal$pheno$freq
state1 state2
HEM3 0.5039526 0.4960474
BAP2 0.4999656 0.5000344
ERG9 0.5000000 0.5000000
PHA2 0.4936116 0.5063884
ERG6 0.5002913 0.4997087
ERG12 0.4916185 0.5083815
TAT1 0.4918805 0.5081195
FLX1 0.4837346 0.5162654
MSY1 0.4986926 0.5013074
GRX5 0.4954240 0.5045760
VMA13 0.4847549 0.5152451
LAT1 0.4891775 0.5108225
NCP1 0.4980495 0.5019505
SLM5 0.4889688 0.5110312
MSE1 0.4803879 0.5196121
ALD6 0.5068041 0.4931959
HIS3 0.4800730 0.5199270
NAM2 0.4994494 0.5005506
ACS1 0.5035334 0.4964666
YNL045W 0.4696969 0.5303031
RBK1 0.4972920 0.5027080
YMR293C 0.5020335 0.4979665
LCB4 0.5026162 0.4973838
PPA2 0.4992428 0.5007572
DIA4 0.4925145 0.5074855
MIR1 0.4923761 0.5076239
YEL047C 0.5004669 0.4995331
MSK1 0.4990194 0.5009806
TRP3 0.4886132 0.5113868
THI22 0.4991591 0.5008409
TNA1 0.4956313 0.5043687
MSD1 0.4933935 0.5066065
YER152C 0.5030933 0.4969067
TAT2 0.4997837 0.5002163
TYS1 0.4989861 0.5010139
YAT2 0.4900365 0.5099635
YEL041W 0.5000000 0.5000000
COX10 0.5025881 0.4974119
$marginal$geno
$marginal$geno$freq
state1 state2
Qchr4 0.5000000 0.5000000
Qchr3 0.4642857 0.5357143
Qchr12 0.4553571 0.5446429
Qchr14 0.4910714 0.5089286
Qchr2 0.5714286 0.4285714
Qchr5 0.6875000 0.3125000
Qchr9 0.4732143 0.5267857
Qchr16 0.5267857 0.4732143
Qchr8 0.6071429 0.3928571
Qchr13 0.4910714 0.5089286
Qchr1 0.5000000 0.5000000
Qchr15 0.4732143 0.5267857
$dbn_nodes
node class levels type
[1,] "HEM3" "factor" "2" "pheno"
[2,] "BAP2" "factor" "2" "pheno"
[3,] "ERG9" "factor" "2" "pheno"
[4,] "PHA2" "factor" "2" "pheno"
[5,] "ERG6" "factor" "2" "pheno"
[6,] "ERG12" "factor" "2" "pheno"
[7,] "TAT1" "factor" "2" "pheno"
[8,] "FLX1" "factor" "2" "pheno"
[9,] "MSY1" "factor" "2" "pheno"
[10,] "GRX5" "factor" "2" "pheno"
[11,] "VMA13" "factor" "2" "pheno"
[12,] "LAT1" "factor" "2" "pheno"
[13,] "NCP1" "factor" "2" "pheno"
[14,] "SLM5" "factor" "2" "pheno"
[15,] "MSE1" "factor" "2" "pheno"
[16,] "ALD6" "factor" "2" "pheno"
[17,] "HIS3" "factor" "2" "pheno"
[18,] "NAM2" "factor" "2" "pheno"
[19,] "ACS1" "factor" "2" "pheno"
[20,] "YNL045W" "factor" "2" "pheno"
[21,] "RBK1" "factor" "2" "pheno"
[22,] "YMR293C" "factor" "2" "pheno"
[23,] "LCB4" "factor" "2" "pheno"
[24,] "PPA2" "factor" "2" "pheno"
[25,] "DIA4" "factor" "2" "pheno"
[26,] "MIR1" "factor" "2" "pheno"
[27,] "YEL047C" "factor" "2" "pheno"
[28,] "MSK1" "factor" "2" "pheno"
[29,] "TRP3" "factor" "2" "pheno"
[30,] "THI22" "factor" "2" "pheno"
[31,] "TNA1" "factor" "2" "pheno"
[32,] "MSD1" "factor" "2" "pheno"
[33,] "YER152C" "factor" "2" "pheno"
[34,] "TAT2" "factor" "2" "pheno"
[35,] "TYS1" "factor" "2" "pheno"
[36,] "YAT2" "factor" "2" "pheno"
[37,] "YEL041W" "factor" "2" "pheno"
[38,] "COX10" "factor" "2" "pheno"
[39,] "Qchr4" "factor" "2" "geno"
[40,] "Qchr3" "factor" "2" "geno"
[41,] "Qchr12" "factor" "2" "geno"
[42,] "Qchr14" "factor" "2" "geno"
[43,] "Qchr2" "factor" "2" "geno"
[44,] "Qchr5" "factor" "2" "geno"
[45,] "Qchr9" "factor" "2" "geno"
[46,] "Qchr16" "factor" "2" "geno"
[47,] "Qchr8" "factor" "2" "geno"
[48,] "Qchr13" "factor" "2" "geno"
[49,] "Qchr1" "factor" "2" "geno"
[50,] "Qchr15" "factor" "2" "geno"
$dbn_flag
[1] "dbn"
attr(,"class")
[1] "dbnfit"
geneNetBP documentation built on May 2, 2019, 5:19 p.m.
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Description Usage Format Details Source Examples
Description
eQTL data from 112 F1 segregants from a cross between BY4716 and RM11-1a strains of Saccharomyces Cerevisiae.
Usage
1 |
Format
The data set yeast is a data frame of 112 observations of 50 variables: genotype data (genotype states at 12 SNP markers) and phenotype data (normalized and discretized expression values of 38 genes). Both genotypes and phenotypes are of class factor.
Details
The yeast dataset is a subset of the widely studied yeast expression dataset comprising of 112 F1 segregants from a cross between BY4716 and RM11-1a strains of Saccharomyces Cerevisiae. The original dataset consists of expression values reported as log2(sample/ BY reference) for 6216 genes. The data can be accessed in Gene Expression Omnibus (GEO) by accession number (GSE1990). After linkage analysis and filtering based on location and significance of QTL, a final set of 38 genes and their corresponding 12 SNP markers were identified and included in the yeast dataset. The gene expression values are discretized around the median and have two states, 1 (above or equal to median) and -1 (below median). There are two genotype states: 1 or 2.\
Thus the final dataset is a data frame of 112 observations (genotype) of 12 variables (SNP markers) and normalized gene expression of 38 variables (genes).\
Source
Brem RB, Kruglyak L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 2005 Feb 1;102(5):1572-7.\
Brem RB, Storey JD, Whittle J, Kruglyak L. Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 2005 Aug 4;436(7051):701-3.\
Examples
1 2 3 4 5 6 |
Example output
Loading required package: Rgraphviz
Loading required package: graph
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, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: grid
Loading required package: bnlearn
Attaching package: 'bnlearn'
The following object is masked from 'package:BiocGenerics':
score
The following object is masked from 'package:stats':
sigma
Loading required package: gRain
Loading required package: gRbase
Attaching package: 'gRbase'
The following objects are masked from 'package:bnlearn':
ancestors, children, parents
$dbn
Bayesian network parameters
Parameters of node HEM3 (multinomial distribution)
Conditional probability table:
, , Qchr4 = 1
YNL045W
HEM3 -1 1
-1 0.8695652 1.0000000
1 0.1304348 0.0000000
, , Qchr4 = 2
YNL045W
HEM3 -1 1
-1 0.0000000 0.1304348
1 1.0000000 0.8695652
Parameters of node BAP2 (multinomial distribution)
Conditional probability table:
, , Qchr2 = 1
Qchr3
BAP2 1 2
-1 0.00000000 0.80645161
1 1.00000000 0.19354839
, , Qchr2 = 2
Qchr3
BAP2 1 2
-1 0.15789474 0.96551724
1 0.84210526 0.03448276
Parameters of node ERG9 (multinomial distribution)
Conditional probability table:
Qchr12
ERG9 1 2
-1 0.07843137 0.85245902
1 0.92156863 0.14754098
Parameters of node PHA2 (multinomial distribution)
Conditional probability table:
, , MSY1 = -1, Qchr14 = 1
BAP2
PHA2 -1 1
-1 0.4375000 0.0000000
1 0.5625000 1.0000000
, , MSY1 = 1, Qchr14 = 1
BAP2
PHA2 -1 1
-1 0.0000000 0.0000000
1 1.0000000 1.0000000
, , MSY1 = -1, Qchr14 = 2
BAP2
PHA2 -1 1
-1 0.8571429 1.0000000
1 0.1428571 0.0000000
, , MSY1 = 1, Qchr14 = 2
BAP2
PHA2 -1 1
-1 1.0000000 0.6000000
1 0.0000000 0.4000000
Parameters of node ERG6 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1
LCB4
ERG6 -1 1
-1 0.0000000 0.1351351
1 1.0000000 0.8648649
, , Qchr12 = 2
LCB4
ERG6 -1 1
-1 0.7619048 1.0000000
1 0.2380952 0.0000000
Parameters of node ERG12 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1
YEL047C
ERG12 -1 1
-1 0.2903226 0.0000000
1 0.7096774 1.0000000
, , Qchr12 = 2
YEL047C
ERG12 -1 1
-1 0.8400000 0.7222222
1 0.1600000 0.2777778
Parameters of node TAT1 (multinomial distribution)
Conditional probability table:
, , Qchr5 = 1
Qchr2
TAT1 1 2
-1 0.91489362 0.20000000
1 0.08510638 0.80000000
, , Qchr5 = 2
Qchr2
TAT1 1 2
-1 0.41176471 0.00000000
1 0.58823529 1.00000000
Parameters of node FLX1 (multinomial distribution)
Conditional probability table:
, , Qchr9 = 1
MSE1
FLX1 -1 1
-1 1.0000000 0.5909091
1 0.0000000 0.4090909
, , Qchr9 = 2
MSE1
FLX1 -1 1
-1 0.2800000 0.1470588
1 0.7200000 0.8529412
Parameters of node MSY1 (multinomial distribution)
Conditional probability table:
GRX5
MSY1 -1 1
-1 0.6428571 0.3571429
1 0.3571429 0.6428571
Parameters of node GRX5 (multinomial distribution)
Conditional probability table:
, , Qchr16 = 1
YAT2
GRX5 -1 1
-1 0.7105263 0.9047619
1 0.2894737 0.0952381
, , Qchr16 = 2
YAT2
GRX5 -1 1
-1 0.0000000 0.2857143
1 1.0000000 0.7142857
Parameters of node VMA13 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
YNL045W
VMA13 -1 1
-1 0.4117647 0.2051282
1 0.5882353 0.7948718
, , COX10 = 1
YNL045W
VMA13 -1 1
-1 0.8717949 0.4117647
1 0.1282051 0.5882353
Parameters of node LAT1 (multinomial distribution)
Conditional probability table:
YNL045W
LAT1 -1 1
-1 0.6785714 0.3214286
1 0.3214286 0.6785714
Parameters of node NCP1 (multinomial distribution)
Conditional probability table:
, , Qchr8 = 1
MSY1
NCP1 -1 1
-1 0.6571429 0.7575758
1 0.3428571 0.2424242
, , Qchr8 = 2
MSY1
NCP1 -1 1
-1 0.0000000 0.3478261
1 1.0000000 0.6521739
Parameters of node SLM5 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
YAT2
SLM5 -1 1
-1 0.7391304 1.0000000
1 0.2608696 0.0000000
, , COX10 = 1
YAT2
SLM5 -1 1
-1 0.1818182 0.0000000
1 0.8181818 1.0000000
Parameters of node MSE1 (multinomial distribution)
Conditional probability table:
, , MSK1 = -1
DIA4
MSE1 -1 1
-1 0.95238095 0.42857143
1 0.04761905 0.57142857
, , MSK1 = 1
DIA4
MSE1 -1 1
-1 0.28571429 0.14285714
1 0.71428571 0.85714286
Parameters of node ALD6 (multinomial distribution)
Conditional probability table:
, , Qchr12 = 1, Qchr13 = 1
Qchr3
ALD6 1 2
-1 0.27272727 0.07142857
1 0.72727273 0.92857143
, , Qchr12 = 2, Qchr13 = 1
Qchr3
ALD6 1 2
-1 0.83333333 0.11111111
1 0.16666667 0.88888889
, , Qchr12 = 1, Qchr13 = 2
Qchr3
ALD6 1 2
-1 0.41666667 0.57142857
1 0.58333333 0.42857143
, , Qchr12 = 2, Qchr13 = 2
Qchr3
ALD6 1 2
-1 1.00000000 0.71428571
1 0.00000000 0.28571429
Parameters of node HIS3 (multinomial distribution)
Conditional probability table:
, , Qchr13 = 1
BAP2
HIS3 -1 1
-1 0.9062500 0.1304348
1 0.0937500 0.8695652
, , Qchr13 = 2
BAP2
HIS3 -1 1
-1 0.5833333 0.3030303
1 0.4166667 0.6969697
Parameters of node NAM2 (multinomial distribution)
Conditional probability table:
, , TYS1 = -1
MSY1
NAM2 -1 1
-1 0.68421053 0.08108108
1 0.31578947 0.91891892
, , TYS1 = 1
MSY1
NAM2 -1 1
-1 0.91891892 0.31578947
1 0.08108108 0.68421053
Parameters of node ACS1 (multinomial distribution)
Conditional probability table:
, , Qchr1 = 1
TYS1
ACS1 -1 1
-1 0.44827586 0.96296296
1 0.55172414 0.03703704
, , Qchr1 = 2
TYS1
ACS1 -1 1
-1 0.22222222 0.37931034
1 0.77777778 0.62068966
Parameters of node YNL045W (multinomial distribution)
Conditional probability table:
, , ACS1 = -1, RBK1 = -1
SLM5
YNL045W -1 1
-1 0.91666667 1.00000000
1 0.08333333 0.00000000
, , ACS1 = 1, RBK1 = -1
SLM5
YNL045W -1 1
-1 0.00000000 0.63636364
1 1.00000000 0.36363636
, , ACS1 = -1, RBK1 = 1
SLM5
YNL045W -1 1
-1 0.47619048 0.00000000
1 0.52380952 1.00000000
, , ACS1 = 1, RBK1 = 1
SLM5
YNL045W -1 1
-1 0.00000000 0.27272727
1 1.00000000 0.72727273
Parameters of node RBK1 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
MSY1
RBK1 -1 1
-1 0.2352941 0.0000000
1 0.7647059 1.0000000
, , COX10 = 1
MSY1
RBK1 -1 1
-1 0.2000000 0.8431373
1 0.8000000 0.1568627
Parameters of node YMR293C (multinomial distribution)
Conditional probability table:
COX10
YMR293C -1 1
-1 0.8928571 0.1071429
1 0.1071429 0.8928571
Parameters of node LCB4 (multinomial distribution)
Conditional probability table:
, , Qchr2 = 1
Qchr12
LCB4 1 2
-1 0.06451613 0.51515152
1 0.93548387 0.48484848
, , Qchr2 = 2
Qchr12
LCB4 1 2
-1 0.60000000 0.89285714
1 0.40000000 0.10714286
Parameters of node PPA2 (multinomial distribution)
Conditional probability table:
, , YAT2 = -1
MSY1
PPA2 -1 1
-1 0.64000000 0.12903226
1 0.36000000 0.87096774
, , YAT2 = 1
MSY1
PPA2 -1 1
-1 0.96774194 0.24000000
1 0.03225806 0.76000000
Parameters of node DIA4 (multinomial distribution)
Conditional probability table:
SLM5
DIA4 -1 1
-1 0.8392857 0.1607143
1 0.1607143 0.8392857
Parameters of node MIR1 (multinomial distribution)
Conditional probability table:
, , Qchr15 = 1
PPA2
MIR1 -1 1
-1 0.4761905 0.1562500
1 0.5238095 0.8437500
, , Qchr15 = 2
PPA2
MIR1 -1 1
-1 0.8857143 0.4166667
1 0.1142857 0.5833333
Parameters of node YEL047C (multinomial distribution)
Conditional probability table:
MSY1
YEL047C -1 1
-1 0.3214286 0.6785714
1 0.6785714 0.3214286
Parameters of node MSK1 (multinomial distribution)
Conditional probability table:
MSY1
MSK1 -1 1
-1 0.875 0.125
1 0.125 0.875
Parameters of node TRP3 (multinomial distribution)
Conditional probability table:
HIS3
TRP3 -1 1
-1 0.7857143 0.2142857
1 0.2142857 0.7857143
Parameters of node THI22 (multinomial distribution)
Conditional probability table:
LCB4
THI22 -1 1
-1 0.3392857 0.6607143
1 0.6607143 0.3392857
Parameters of node TNA1 (multinomial distribution)
Conditional probability table:
, , RBK1 = -1
ACS1
TNA1 -1 1
-1 0.6333333 0.1153846
1 0.3666667 0.8846154
, , RBK1 = 1
ACS1
TNA1 -1 1
-1 0.7692308 0.4666667
1 0.2307692 0.5333333
Parameters of node MSD1 (multinomial distribution)
Conditional probability table:
, , COX10 = -1
MSK1
MSD1 -1 1
-1 0.93617021 0.22222222
1 0.06382979 0.77777778
, , COX10 = 1
MSK1
MSD1 -1 1
-1 0.44444444 0.12765957
1 0.55555556 0.87234043
Parameters of node YER152C (multinomial distribution)
Conditional probability table:
, , Qchr4 = 1
NCP1
YER152C -1 1
-1 0.8064516 0.4800000
1 0.1935484 0.5200000
, , Qchr4 = 2
NCP1
YER152C -1 1
-1 0.6000000 0.1290323
1 0.4000000 0.8709677
Parameters of node TAT2 (multinomial distribution)
Conditional probability table:
NAM2
TAT2 -1 1
-1 0.6964286 0.3035714
1 0.3035714 0.6964286
Parameters of node TYS1 (multinomial distribution)
Conditional probability table:
, , TRP3 = -1
PPA2
TYS1 -1 1
-1 0.5000000 0.8529412
1 0.5000000 0.1470588
, , TRP3 = 1
PPA2
TYS1 -1 1
-1 0.1176471 0.5454545
1 0.8823529 0.4545455
Parameters of node YAT2 (multinomial distribution)
Conditional probability table:
HIS3
YAT2 -1 1
-1 0.75 0.25
1 0.25 0.75
Parameters of node YEL041W (multinomial distribution)
Conditional probability table:
-1 1
0.5 0.5
Parameters of node COX10 (multinomial distribution)
Conditional probability table:
, , TAT2 = -1
MSY1
COX10 -1 1
-1 0.91891892 0.26315789
1 0.08108108 0.73684211
, , TAT2 = 1
MSY1
COX10 -1 1
-1 0.89473684 0.00000000
1 0.10526316 1.00000000
Parameters of node Qchr4 (multinomial distribution)
Conditional probability table:
1 2
0.5 0.5
Parameters of node Qchr3 (multinomial distribution)
Conditional probability table:
1 2
0.4642857 0.5357143
Parameters of node Qchr12 (multinomial distribution)
Conditional probability table:
1 2
0.4553571 0.5446429
Parameters of node Qchr14 (multinomial distribution)
Conditional probability table:
1 2
0.4910714 0.5089286
Parameters of node Qchr2 (multinomial distribution)
Conditional probability table:
1 2
0.5714286 0.4285714
Parameters of node Qchr5 (multinomial distribution)
Conditional probability table:
1 2
0.6875 0.3125
Parameters of node Qchr9 (multinomial distribution)
Conditional probability table:
1 2
0.4732143 0.5267857
Parameters of node Qchr16 (multinomial distribution)
Conditional probability table:
1 2
0.5267857 0.4732143
Parameters of node Qchr8 (multinomial distribution)
Conditional probability table:
1 2
0.6071429 0.3928571
Parameters of node Qchr13 (multinomial distribution)
Conditional probability table:
1 2
0.4910714 0.5089286
Parameters of node Qchr1 (multinomial distribution)
Conditional probability table:
1 2
0.5 0.5
Parameters of node Qchr15 (multinomial distribution)
Conditional probability table:
1 2
0.4732143 0.5267857
$marginal
$marginal$pheno
$marginal$pheno$freq
state1 state2
HEM3 0.5039526 0.4960474
BAP2 0.4999656 0.5000344
ERG9 0.5000000 0.5000000
PHA2 0.4936116 0.5063884
ERG6 0.5002913 0.4997087
ERG12 0.4916185 0.5083815
TAT1 0.4918805 0.5081195
FLX1 0.4837346 0.5162654
MSY1 0.4986926 0.5013074
GRX5 0.4954240 0.5045760
VMA13 0.4847549 0.5152451
LAT1 0.4891775 0.5108225
NCP1 0.4980495 0.5019505
SLM5 0.4889688 0.5110312
MSE1 0.4803879 0.5196121
ALD6 0.5068041 0.4931959
HIS3 0.4800730 0.5199270
NAM2 0.4994494 0.5005506
ACS1 0.5035334 0.4964666
YNL045W 0.4696969 0.5303031
RBK1 0.4972920 0.5027080
YMR293C 0.5020335 0.4979665
LCB4 0.5026162 0.4973838
PPA2 0.4992428 0.5007572
DIA4 0.4925145 0.5074855
MIR1 0.4923761 0.5076239
YEL047C 0.5004669 0.4995331
MSK1 0.4990194 0.5009806
TRP3 0.4886132 0.5113868
THI22 0.4991591 0.5008409
TNA1 0.4956313 0.5043687
MSD1 0.4933935 0.5066065
YER152C 0.5030933 0.4969067
TAT2 0.4997837 0.5002163
TYS1 0.4989861 0.5010139
YAT2 0.4900365 0.5099635
YEL041W 0.5000000 0.5000000
COX10 0.5025881 0.4974119
$marginal$geno
$marginal$geno$freq
state1 state2
Qchr4 0.5000000 0.5000000
Qchr3 0.4642857 0.5357143
Qchr12 0.4553571 0.5446429
Qchr14 0.4910714 0.5089286
Qchr2 0.5714286 0.4285714
Qchr5 0.6875000 0.3125000
Qchr9 0.4732143 0.5267857
Qchr16 0.5267857 0.4732143
Qchr8 0.6071429 0.3928571
Qchr13 0.4910714 0.5089286
Qchr1 0.5000000 0.5000000
Qchr15 0.4732143 0.5267857
$dbn_nodes
node class levels type
[1,] "HEM3" "factor" "2" "pheno"
[2,] "BAP2" "factor" "2" "pheno"
[3,] "ERG9" "factor" "2" "pheno"
[4,] "PHA2" "factor" "2" "pheno"
[5,] "ERG6" "factor" "2" "pheno"
[6,] "ERG12" "factor" "2" "pheno"
[7,] "TAT1" "factor" "2" "pheno"
[8,] "FLX1" "factor" "2" "pheno"
[9,] "MSY1" "factor" "2" "pheno"
[10,] "GRX5" "factor" "2" "pheno"
[11,] "VMA13" "factor" "2" "pheno"
[12,] "LAT1" "factor" "2" "pheno"
[13,] "NCP1" "factor" "2" "pheno"
[14,] "SLM5" "factor" "2" "pheno"
[15,] "MSE1" "factor" "2" "pheno"
[16,] "ALD6" "factor" "2" "pheno"
[17,] "HIS3" "factor" "2" "pheno"
[18,] "NAM2" "factor" "2" "pheno"
[19,] "ACS1" "factor" "2" "pheno"
[20,] "YNL045W" "factor" "2" "pheno"
[21,] "RBK1" "factor" "2" "pheno"
[22,] "YMR293C" "factor" "2" "pheno"
[23,] "LCB4" "factor" "2" "pheno"
[24,] "PPA2" "factor" "2" "pheno"
[25,] "DIA4" "factor" "2" "pheno"
[26,] "MIR1" "factor" "2" "pheno"
[27,] "YEL047C" "factor" "2" "pheno"
[28,] "MSK1" "factor" "2" "pheno"
[29,] "TRP3" "factor" "2" "pheno"
[30,] "THI22" "factor" "2" "pheno"
[31,] "TNA1" "factor" "2" "pheno"
[32,] "MSD1" "factor" "2" "pheno"
[33,] "YER152C" "factor" "2" "pheno"
[34,] "TAT2" "factor" "2" "pheno"
[35,] "TYS1" "factor" "2" "pheno"
[36,] "YAT2" "factor" "2" "pheno"
[37,] "YEL041W" "factor" "2" "pheno"
[38,] "COX10" "factor" "2" "pheno"
[39,] "Qchr4" "factor" "2" "geno"
[40,] "Qchr3" "factor" "2" "geno"
[41,] "Qchr12" "factor" "2" "geno"
[42,] "Qchr14" "factor" "2" "geno"
[43,] "Qchr2" "factor" "2" "geno"
[44,] "Qchr5" "factor" "2" "geno"
[45,] "Qchr9" "factor" "2" "geno"
[46,] "Qchr16" "factor" "2" "geno"
[47,] "Qchr8" "factor" "2" "geno"
[48,] "Qchr13" "factor" "2" "geno"
[49,] "Qchr1" "factor" "2" "geno"
[50,] "Qchr15" "factor" "2" "geno"
$dbn_flag
[1] "dbn"
attr(,"class")
[1] "dbnfit"
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