get.verhaak.subtypes: Get ovarian cancer subtypes as defined by Verhaak et al.,...

In consensusOV: Gene expression-based subtype classification for high-grade serous ovarian cancer

Description

Get ovarian cancer subtypes as defined by Verhaak et al., 2013

Usage

get.verhaak.subtypes(expression.matrix, entrez.ids)

Arguments

expression.matrix	A matrix of gene expression values with rows as genes, columns as samples.
entrez.ids	A vector of Entrez Gene IDs, corresponding to the rows of expression.matrix

Value

A list with first value Verhaak.subtypes containing a factor of subtype names; and second value gsva containing the GSVA subtype scores

References

Verhaak et al. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. The Journal of Clinical Investigation (2013)

Examples

library(Biobase)
data(GSE14764.eset)
expression.matrix <- exprs(GSE14764.eset)
entrez.ids <- as.character(fData(GSE14764.eset)$EntrezGene.ID)
get.konecny.subtypes(expression.matrix, entrez.ids)

Example output

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’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, 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")'.

$Konecny.subtypes
 [1] C3_profL C1_immL  C2_diffL C4_mescL C1_immL  C1_immL  C4_mescL C3_profL
 [9] C3_profL C1_immL  C2_diffL C2_diffL C4_mescL C2_diffL C3_profL C2_diffL
[17] C1_immL  C4_mescL C1_immL  C2_diffL C4_mescL C4_mescL C4_mescL C1_immL 
[25] C3_profL C3_profL C2_diffL C2_diffL C3_profL C2_diffL C3_profL C1_immL 
[33] C1_immL  C2_diffL C1_immL  C2_diffL C3_profL C3_profL C2_diffL C3_profL
[41] C2_diffL
Levels: C1_immL C2_diffL C3_profL C4_mescL

$spearman.cc.vals
                         C1_immL     C2_diffL    C3_profL    C4_mescL
GSE14764_GSM368661 -0.2868336632 -0.014459967  0.34205354  0.17161226
GSE14764_GSM368662  0.6779956799 -0.262306179 -0.62366552  0.06016172
GSE14764_GSM368664 -0.3581646706  0.325955130  0.27893418 -0.31239446
GSE14764_GSM368665  0.0972350813 -0.132512162 -0.15056511  0.24325904
GSE14764_GSM368668  0.5722580671 -0.536407982 -0.23860287  0.50150221
GSE14764_GSM368670  0.5350106598 -0.254001785 -0.48192535  0.04694500
GSE14764_GSM368671 -0.1151397014 -0.017518583  0.03822365  0.12077674
GSE14764_GSM368673 -0.1690761923 -0.110183226  0.35963556  0.20949403
GSE14764_GSM368675 -0.1669524666 -0.006446259  0.28340226  0.06258557
GSE14764_GSM368678  0.7977355491 -0.552552838 -0.52591431  0.35570730
GSE14764_GSM368679 -0.2709796962  0.344578436  0.09921367 -0.33074855
GSE14764_GSM368681 -0.0474818021  0.179847226 -0.09953687 -0.27790213
GSE14764_GSM368683 -0.0536128833 -0.354217812  0.31552273  0.59018116
GSE14764_GSM368685 -0.3180756584  0.267474468  0.24666114 -0.27205912
GSE14764_GSM368689 -0.3968225417  0.265651866  0.34670229 -0.24677356
GSE14764_GSM368691  0.0012334031  0.145792125 -0.11449008 -0.24649913
GSE14764_GSM368692  0.3643318866 -0.243253270 -0.22050432  0.13057651
GSE14764_GSM368694  0.2123366403 -0.551942761  0.14242955  0.70989553
GSE14764_GSM368695  0.3262011828  0.011940765 -0.44658305 -0.20601204
GSE14764_GSM368698 -0.2962080484  0.312533839  0.15882915 -0.33742768
GSE14764_GSM368699  0.1434884991 -0.373344998  0.04112869  0.54080328
GSE14764_GSM368700 -0.1267905825 -0.074716858  0.07527312  0.23273858
GSE14764_GSM368703 -0.0827959947 -0.151538372  0.21473238  0.21780946
GSE14764_GSM368707  0.1367268647 -0.002217878 -0.13406654  0.01595976
GSE14764_GSM368709 -0.3941435437  0.203000639  0.25979154 -0.18091859
GSE14764_GSM368710 -0.0582708669 -0.119145475  0.19078521  0.17666712
GSE14764_GSM368714 -0.5283200906  0.466448881  0.36384728 -0.31852413
GSE14764_GSM368715 -0.0072412242  0.022030020 -0.01177715 -0.03255128
GSE14764_GSM368720 -0.4059050376  0.244694449  0.39337227 -0.14593463
GSE14764_GSM368721 -0.2914143584  0.522222037 -0.01440235 -0.52740066
GSE14764_GSM368722 -0.4956353110  0.318832346  0.36576062 -0.27806715
GSE14764_GSM368723  0.2817121497 -0.258576861 -0.17037424  0.23614610
GSE14764_GSM368724  0.5754875194 -0.206830934 -0.61619825 -0.01283028
GSE14764_GSM368725 -0.0532334673  0.343040696 -0.16794597 -0.52699013
GSE14764_GSM368726  0.1959053186  0.111022157 -0.37409693 -0.30055587
GSE14764_GSM368728  0.0067526007  0.183580760 -0.19934636 -0.17157050
GSE14764_GSM368731 -0.1311946183 -0.088574377  0.27226570  0.22478369
GSE14764_GSM368732 -0.2128999426 -0.118311161  0.30803760  0.30292532
GSE14764_GSM368734 -0.0001471492  0.172953899 -0.08901079 -0.37130933
GSE14764_GSM368736 -0.1419788651 -0.054210725  0.19474920  0.14330542
GSE14764_GSM368737 -0.2446418032  0.366918814  0.03933038 -0.37556541

consensusOV documentation built on Nov. 8, 2020, 7:06 p.m.