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Question: LuminalA Breast cancer subtype samples from GEO GSE62944
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gravatar for hamda.binte.ajmal
19 months ago by
hamda.binte.ajmal0 wrote:

Hi All,

is there a way to pull out samples of Luminal A subtype of breast cancer from TCGA data or GEO GSE62944?

I did 

    library(AnnotationHub)
    eh = AnnotationHub()
    query(eh , "GSE62944")
    tcga_data <- eh[["AH28855"]]

    brca_data_lumA <- brca_data[, which(phenoData(brca_data)$er_status_by_ihc=="Positive")]
    brca_data_lumA <- brca_data[, which(phenoData(brca_data)$her2_status_by_ihc=="Negative")]

 

Considering Luminal A subtype = ER Positive, Her2 Negative and low ki67 !

I do not know how to determine samples with low ki67 ?

Is there a better way to do it? Is there a predefined attribute dedicated to molecular subtype of Breast Cancer?

ADD COMMENTlink modified 19 months ago by phil.chapman120 • written 19 months ago by hamda.binte.ajmal0
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gravatar for phil.chapman
19 months ago by
phil.chapman120
United Kingdom
phil.chapman120 wrote:

Not sure how to do it in Bioconductor but the cgdsr package (from CRAN) that accompanies the cBio Portal has some useful pre-defined sets of cases that relate to different breast cancer subtypes.  I think that these have been manually curated from the original publication.  Anyway, take a look at the cBio Portal itself and the cgdsr package documentation, and perhaps you can incorporate this information into your analysis to do what you want.  An example is below:

> library(cgdsr)
> mycgds <- CGDS("http://www.cbioportal.org/")
> getCancerStudies(mycgds)[1:10,1]
 [1] "paac_jhu_2014"                 "laml_tcga_pub"                 "laml_tcga"                    
 [4] "acyc_mskcc"                    "acc_tcga"                      "blca_mskcc_solit_2014"        
 [7] "blca_mskcc_solit_2012"         "blca_mskcc_signet_ring_impact" "blca_plasmacytoid_mskcc_2016"
[10] "blca_bgi" 
> brca_case_lists <- getCaseLists(mycgds,'brca_tcga_pub2015')
> brca_case_lists[1:5,1:2]
                     case_list_id              case_list_name
1 brca_tcga_pub2015_3way_complete         All Complete Tumors
2           brca_tcga_pub2015_all                  All Tumors
3         brca_tcga_pub2015_erpos           ER+ breast tumors
4         brca_tcga_pub2015_erneg           ER- breast tumors
5       brca_tcga_pub2015_her2pos Her2-positive breast tumors

> substr(brca_case_lists[brca_case_lists$case_list_id == 'brca_tcga_pub2015_idc_luma', 'case_ids'], 1, 80)
[1] "TCGA-BH-A1ES-01 TCGA-BH-A1ET-01 TCGA-BH-A1EW-01 TCGA-C8-A1HI-01 TCGA-A2-A1G0-01 "

 

ADD COMMENTlink written 19 months ago by phil.chapman120
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