Package STROMA4. October 22, 2018
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1 Version Date Title Assign Properties to TNBC Patients Package STROMA4 October 22, 2018 This package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer (TNBC) patients and represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D). Additionally this package can also be used to estimate generative properties for the Lehmann subtypes, an alternative TNBC subtyping scheme (PMID: ). Depends R (>= 3.4), Biobase, BiocParallel, cluster, matrixstats, stats, graphics, utils License GPL-3 LazyData true RoxygenNote Suggests breastcancermainz biocviews GeneExpression, BiomedicalInformatics, Classification, Microarray, RNASeq, Software git_url git_branch master git_last_commit 0d07247 git_last_commit_date Date/Publication Author Sadiq Saleh [aut, cre], Michael Hallett [aut] Maintainer Sadiq Saleh <sadiq.mehdiismailsaleh@mail.mcgill.ca> R topics documented: assign.properties B.stroma.property
2 2 assign.properties BL1.property BL2.property D.stroma.property E.stroma.property IM.property LAR.property M.property MSL.property T.stroma.property Index 10 assign.properties Function to assign properties to an expression matrix assign.properties is a function to assign stromal property and Lehmann generative property levels to a TNBC dataset. Given an expressionset with a gene expression matrix, and a a list of HGNC IDs, this function will estimate the status of samples for either the Lehmann generative properties, the stromal properties, or both at the same time. (Saleh et al., under review at Cancer Research) assign.properties(eset, geneid.column = 1, genelists = c("stroma4", "TNBCType"), n = 1000, seed = , mc.cores = snowworkers(), var.method = function(x) rowiqrs(x, na.rm = TRUE)) Arguments ESet geneid.column genelists n seed mc.cores var.method An ExpressionSet object. Rows correspond to genes, columns to samples. If there are genes with multiple probes, they will be collapsed to a single row using the function defined in var.method. Integer or column name corresponding to column in featuredata table corresponding to HGNC ID. A vector with either Stroma4, TNBCType, or both to specify which genelists to use. An integer value specifying the number of random samples to generate. An integer value specifying a seed for the random ranks function. Default value is An integer specifying how many cores to use. Defaults to use the function snow- Workers(). Function for assessing variance to collapse probes. Default is IQR
3 B.stroma.property 3 Details We defined a method for estimating stromal and Lehmann generative properties in a gene expression dataset (either LCM stroma or whole tumor breast cancer data). The assign.properties function extracts the expression data from the expression set using the exprs() function. The HGNC ID annotations for the dataset are required as this is what the function uses to identify genes to estimate property levels. The HGNC IDs should be in the featuredata of the expressionset, and the corresponding column ID should be passed to the geneid.column argument. The function can be used to estimate the stromal properties, the Lehmann generative properties or both simultaneously depending on whether STROMA4 (stromal properties), TNBCTYPE (Lehmann generative properties), or both are passed to the genelists argument. This function will then return property assignments. The function returns a the ExpressionSet with the properties added to the pdata table. library(breastcancermainz) data(mainz, package='breastcancermainz') all.properties <- assign.properties(eset=mainz, geneid.column='gene.symbol', genelists=c('stroma4', 'TNBCType'), n=10) B.stroma.property Genelist for B.stroma.property data('b.stroma.property') An object of class data.frame with 567 rows and 2 columns. An object of class data.frame with 567 rows and 2 columns. data('b.stroma.property')
4 4 BL2.property BL1.property Genelist for BL1.property data('bl1.property') An object of class data.frame with 473 rows and 2 columns. An object of class data.frame with 473 rows and 2 columns. data('bl1.property') BL2.property Genelist for BL2.property data('bl2.property') An object of class data.frame with 291 rows and 2 columns. An object of class data.frame with 291 rows and 2 columns.
5 D.stroma.property 5 data('bl2.property') D.stroma.property Genelist for D.stroma.property data('d.stroma.property') An object of class data.frame with 297 rows and 2 columns. An object of class data.frame with 297 rows and 2 columns. data('d.stroma.property')
6 6 IM.property E.stroma.property Genelist for E.stroma.property data('e.stroma.property') An object of class data.frame with 27 rows and 2 columns. An object of class data.frame with 27 rows and 2 columns. data('e.stroma.property') IM.property Genelist for IM.property data('im.property') An object of class data.frame with 705 rows and 2 columns. An object of class data.frame with 705 rows and 2 columns.
7 LAR.property 7 data('im.property') LAR.property Genelist for LAR.property data('lar.property') An object of class data.frame with 1205 rows and 2 columns. An object of class data.frame with 1205 rows and 2 columns. data('lar.property')
8 8 MSL.property M.property Genelist for M.property data('m.property') An object of class data.frame with 710 rows and 2 columns. An object of class data.frame with 710 rows and 2 columns. data('m.property') MSL.property Genelist for MSL.property data('msl.property') An object of class data.frame with 1105 rows and 2 columns. An object of class data.frame with 1105 rows and 2 columns.
9 T.stroma.property 9 data('msl.property') T.stroma.property Genelist for T.stroma.property data('t.stroma.property') An object of class data.frame with 458 rows and 2 columns. An object of class data.frame with 458 rows and 2 columns. data('t.stroma.property')
10 Index Topic List B.stroma.property, 3 BL1.property, 4 BL2.property, 4 D.stroma.property, 5 E.stroma.property, 6 IM.property, 6 LAR.property, 7 M.property, 8 MSL.property, 8 T.stroma.property, 9 assign.properties, 2 B.stroma.property, 3 BL1.property, 4 BL2.property, 4 D.stroma.property, 5 E.stroma.property, 6 IM.property, 6 LAR.property, 7 M.property, 8 MSL.property, 8 T.stroma.property, 9 10
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