AlvMac_results: Sample output from the 'GO_analyse()' function on an RNAseq...
In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations
Description
Usage
Value
Warning
Source
Examples
Description
This variable may be used to test the filtering and visualisation methods
implemented in the package. It contains the output of the command
AlvMac_results = GO_analyse(eSet=AlvMac, f="Treatment")
applied to the toy input data AlvMac.
Usage
1
Value
A list of 9 slots summarising the input and results of the analysis:
GO contains a table ranking all GO terms related to genes in
the expression dataset based on the average ability of their related
genes to cluster the samples according to the predefined grouping
factor.
mapping contains the table mapping genes present in the
dataset to GO terms.
genes contains a table ranking all genes present in the
expression dataset based on their ability to cluster the samples
according to the predefined grouping factor (see 'factor' below).
factor contains the grouping factor analysed.
method contains the statistical framework used.
subset contains the filters used to select a subset of
samples from the original ExpressionSet for analysis.
rank.by contains the metric used to rank the scoring tables.
ntree contains number of trees built during the randomForest
analysis.
mtry contains the number of features randomly sampled as
candidates at each split in each tree built during the randomForest
analysis.
Warning
Running the above command again, you might obtain slightly different scores
and ranks due to the stochastic process of sampling used by the random forest
algorithm. However, the ranking metric was found to be robust and stable
across run, given adequate number of trees and predictor variables sampled.
To produce reproducible results, use the set.seed() function prior
to running any randomising or sampling function.
Source
Source data are part of a publication in review.
Examples
1
2
3
4
data(AlvMac_results)
str(AlvMac_results)
head(AlvMac_results$GO, n=20)
head(AlvMac_results$GO$genes, n=20)
Example output
Loading required package: grid
Loading required package: Biobase
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
List of 9
$ GO :'data.frame': 13302 obs. of 7 variables:
..$ go_id : chr [1:13302] "GO:0004113" "GO:0009214" "GO:0032682" "GO:0070427" ...
..$ ave_rank : num [1:13302] 2 2 7 7.5 11 11 14 18 18 25 ...
..$ ave_score : num [1:13302] 3.46 3.46 1.26 1.69 1 ...
..$ total_count : num [1:13302] 1 1 1 2 1 1 1 1 1 1 ...
..$ data_count : num [1:13302] 1 1 1 2 1 1 1 1 1 1 ...
..$ name_1006 : chr [1:13302] "2',3'-cyclic-nucleotide 3'-phosphodiesterase activity" "cyclic nucleotide catabolic process" "negative regulation of chemokine production" "nucleotide-binding oligomerization domain containing 1 signaling pathway" ...
..$ namespace_1003: chr [1:13302] "molecular_function" "biological_process" "biological_process" "biological_process" ...
$ mapping:'data.frame': 191614 obs. of 2 variables:
..$ gene_id: chr [1:191614] "ENSBTAG00000020495" "ENSBTAG00000020495" "ENSBTAG00000020495" "ENSBTAG00000020495" ...
..$ go_id : chr [1:191614] "GO:0005515" "GO:0006661" "GO:1900027" "GO:0032587" ...
$ genes :'data.frame': 100 obs. of 4 variables:
..$ Score : num [1:100] 7.49 3.46 3.36 2.37 2.33 ...
..$ Rank : int [1:100] 1 2 3 4 5 6 7 8 9 10 ...
..$ external_gene_name: chr [1:100] "TSG-6" "CNP" "TNIP3" "BIKBA" ...
..$ description : chr [1:100] "Bos taurus tumor necrosis factor, alpha-induced protein 6 (TNFAIP6), mRNA. [Source:RefSeq mRNA;Acc:NM_001007813]" "Bos taurus 2',3'-cyclic nucleotide 3' phosphodiesterase (CNP), mRNA. [Source:RefSeq mRNA;Acc:NM_180993]" "TNFAIP3 interacting protein 3 [Source:HGNC Symbol;Acc:HGNC:19315]" "Bos taurus nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (NFKBIA), mRNA. "| __truncated__ ...
$ factor : chr "Treatment"
$ method : chr "randomForest"
$ subset : NULL
$ rank.by: chr "rank"
$ ntree : num 1000
$ mtry : Named num 20
..- attr(*, "names")= chr "Features"
go_id ave_rank ave_score total_count data_count
1308 GO:0004113 2.0 3.4619819 1 1
3498 GO:0009214 2.0 3.4619819 1 1
6341 GO:0032682 7.0 1.2641160 1 1
11129 GO:0070427 7.5 1.6862141 2 2
6532 GO:0033091 11.0 1.0011242 1 1
11216 GO:0070673 11.0 1.0011242 1 1
2090 GO:0005684 14.0 0.9147929 1 1
2629 GO:0006664 18.0 0.8607601 1 1
10193 GO:0052798 18.0 0.8607601 1 1
7053 GO:0035251 25.0 0.7861392 1 1
6364 GO:0032732 32.0 0.7398141 1 1
11132 GO:0070430 32.0 0.7398141 1 1
1635 GO:0004728 33.0 0.7341205 1 1
7891 GO:0042748 36.0 0.6921449 1 1
9751 GO:0050951 36.0 0.6921449 1 1
12403 GO:1900242 36.0 0.6921449 1 1
6992 GO:0035048 38.0 0.6720161 1 1
6756 GO:0034142 40.0 1.3278388 8 7
8887 GO:0046331 44.0 0.5955187 1 1
10839 GO:0061106 44.0 0.5955187 1 1
name_1006
1308 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
3498 cyclic nucleotide catabolic process
6341 negative regulation of chemokine production
11129 nucleotide-binding oligomerization domain containing 1 signaling pathway
6532 positive regulation of immature T cell proliferation
11216 response to interleukin-18
2090 U2-type spliceosomal complex
2629 glycolipid metabolic process
10193 beta-galactoside alpha-2,3-sialyltransferase activity
7053 UDP-glucosyltransferase activity
6364 positive regulation of interleukin-1 production
11132 positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway
1635 receptor signaling protein tyrosine phosphatase activity
7891 circadian sleep/wake cycle, non-REM sleep
9751 sensory perception of temperature stimulus
12403 regulation of synaptic vesicle endocytosis
6992 splicing factor protein import into nucleus
6756 toll-like receptor 4 signaling pathway
8887 lateral inhibition
10839 negative regulation of stomach neuroendocrine cell differentiation
namespace_1003
1308 molecular_function
3498 biological_process
6341 biological_process
11129 biological_process
6532 biological_process
11216 biological_process
2090 cellular_component
2629 biological_process
10193 molecular_function
7053 molecular_function
6364 biological_process
11132 biological_process
1635 molecular_function
7891 biological_process
9751 biological_process
12403 biological_process
6992 biological_process
6756 biological_process
8887 biological_process
10839 biological_process
NULL
GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.
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Description Usage Value Warning Source Examples
Description
This variable may be used to test the filtering and visualisation methods
implemented in the package. It contains the output of the command
AlvMac_results = GO_analyse(eSet=AlvMac, f="Treatment")
applied to the toy input data AlvMac.
Usage
1 |
Value
A list of 9 slots summarising the input and results of the analysis:
GOcontains a table ranking all GO terms related to genes in the expression dataset based on the average ability of their related genes to cluster the samples according to the predefined grouping factor.mappingcontains the table mapping genes present in the dataset to GO terms.genescontains a table ranking all genes present in the expression dataset based on their ability to cluster the samples according to the predefined grouping factor (see 'factor' below).factorcontains the grouping factor analysed.methodcontains the statistical framework used.subsetcontains the filters used to select a subset of samples from the originalExpressionSetfor analysis.rank.bycontains the metric used to rank the scoring tables.ntreecontains number of trees built during the randomForest analysis.mtrycontains the number of features randomly sampled as candidates at each split in each tree built during the randomForest analysis.
Warning
Running the above command again, you might obtain slightly different scores and ranks due to the stochastic process of sampling used by the random forest algorithm. However, the ranking metric was found to be robust and stable across run, given adequate number of trees and predictor variables sampled.
To produce reproducible results, use the set.seed() function prior
to running any randomising or sampling function.
Source
Source data are part of a publication in review.
Examples
1 2 3 4 | data(AlvMac_results)
str(AlvMac_results)
head(AlvMac_results$GO, n=20)
head(AlvMac_results$GO$genes, n=20)
|
Example output
Loading required package: grid
Loading required package: Biobase
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, basename, cbind, colMeans, colSums, colnames,
dirname, 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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
List of 9
$ GO :'data.frame': 13302 obs. of 7 variables:
..$ go_id : chr [1:13302] "GO:0004113" "GO:0009214" "GO:0032682" "GO:0070427" ...
..$ ave_rank : num [1:13302] 2 2 7 7.5 11 11 14 18 18 25 ...
..$ ave_score : num [1:13302] 3.46 3.46 1.26 1.69 1 ...
..$ total_count : num [1:13302] 1 1 1 2 1 1 1 1 1 1 ...
..$ data_count : num [1:13302] 1 1 1 2 1 1 1 1 1 1 ...
..$ name_1006 : chr [1:13302] "2',3'-cyclic-nucleotide 3'-phosphodiesterase activity" "cyclic nucleotide catabolic process" "negative regulation of chemokine production" "nucleotide-binding oligomerization domain containing 1 signaling pathway" ...
..$ namespace_1003: chr [1:13302] "molecular_function" "biological_process" "biological_process" "biological_process" ...
$ mapping:'data.frame': 191614 obs. of 2 variables:
..$ gene_id: chr [1:191614] "ENSBTAG00000020495" "ENSBTAG00000020495" "ENSBTAG00000020495" "ENSBTAG00000020495" ...
..$ go_id : chr [1:191614] "GO:0005515" "GO:0006661" "GO:1900027" "GO:0032587" ...
$ genes :'data.frame': 100 obs. of 4 variables:
..$ Score : num [1:100] 7.49 3.46 3.36 2.37 2.33 ...
..$ Rank : int [1:100] 1 2 3 4 5 6 7 8 9 10 ...
..$ external_gene_name: chr [1:100] "TSG-6" "CNP" "TNIP3" "BIKBA" ...
..$ description : chr [1:100] "Bos taurus tumor necrosis factor, alpha-induced protein 6 (TNFAIP6), mRNA. [Source:RefSeq mRNA;Acc:NM_001007813]" "Bos taurus 2',3'-cyclic nucleotide 3' phosphodiesterase (CNP), mRNA. [Source:RefSeq mRNA;Acc:NM_180993]" "TNFAIP3 interacting protein 3 [Source:HGNC Symbol;Acc:HGNC:19315]" "Bos taurus nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (NFKBIA), mRNA. "| __truncated__ ...
$ factor : chr "Treatment"
$ method : chr "randomForest"
$ subset : NULL
$ rank.by: chr "rank"
$ ntree : num 1000
$ mtry : Named num 20
..- attr(*, "names")= chr "Features"
go_id ave_rank ave_score total_count data_count
1308 GO:0004113 2.0 3.4619819 1 1
3498 GO:0009214 2.0 3.4619819 1 1
6341 GO:0032682 7.0 1.2641160 1 1
11129 GO:0070427 7.5 1.6862141 2 2
6532 GO:0033091 11.0 1.0011242 1 1
11216 GO:0070673 11.0 1.0011242 1 1
2090 GO:0005684 14.0 0.9147929 1 1
2629 GO:0006664 18.0 0.8607601 1 1
10193 GO:0052798 18.0 0.8607601 1 1
7053 GO:0035251 25.0 0.7861392 1 1
6364 GO:0032732 32.0 0.7398141 1 1
11132 GO:0070430 32.0 0.7398141 1 1
1635 GO:0004728 33.0 0.7341205 1 1
7891 GO:0042748 36.0 0.6921449 1 1
9751 GO:0050951 36.0 0.6921449 1 1
12403 GO:1900242 36.0 0.6921449 1 1
6992 GO:0035048 38.0 0.6720161 1 1
6756 GO:0034142 40.0 1.3278388 8 7
8887 GO:0046331 44.0 0.5955187 1 1
10839 GO:0061106 44.0 0.5955187 1 1
name_1006
1308 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
3498 cyclic nucleotide catabolic process
6341 negative regulation of chemokine production
11129 nucleotide-binding oligomerization domain containing 1 signaling pathway
6532 positive regulation of immature T cell proliferation
11216 response to interleukin-18
2090 U2-type spliceosomal complex
2629 glycolipid metabolic process
10193 beta-galactoside alpha-2,3-sialyltransferase activity
7053 UDP-glucosyltransferase activity
6364 positive regulation of interleukin-1 production
11132 positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway
1635 receptor signaling protein tyrosine phosphatase activity
7891 circadian sleep/wake cycle, non-REM sleep
9751 sensory perception of temperature stimulus
12403 regulation of synaptic vesicle endocytosis
6992 splicing factor protein import into nucleus
6756 toll-like receptor 4 signaling pathway
8887 lateral inhibition
10839 negative regulation of stomach neuroendocrine cell differentiation
namespace_1003
1308 molecular_function
3498 biological_process
6341 biological_process
11129 biological_process
6532 biological_process
11216 biological_process
2090 cellular_component
2629 biological_process
10193 molecular_function
7053 molecular_function
6364 biological_process
11132 biological_process
1635 molecular_function
7891 biological_process
9751 biological_process
12403 biological_process
6992 biological_process
6756 biological_process
8887 biological_process
10839 biological_process
NULL
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