ALL

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1 Package ‘ALL’ May 2, 2019 A data package Title Version 1.25.0 2009-07-22 Date Author Xiaochun Li Description Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Labora- tory at the DFCI (includes Apr 2004 versions) Maintainer Robert Gentleman License Artistic-2.0 Depends R (>= 2.10), Biobase (>= 2.5.5) Suggests rpart biocViews ExperimentData, CancerData, LeukemiaCancerData git_url https://git.bioconductor.org/packages/ALL git_branch master 826c18c git_last_commit git_last_commit_date 2018-10-30 Date/Publication 2019-05-02 R topics documented: ALL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 tojulian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Index 4 ALL Acute Lymphoblastic Leukemia Data from the Ritz Laboratory Description The data consist of microarrays from 128 different individuals with acute lymphoblastic leukemia (ALL). A number of additional covariates are available. The data have been normalized (using rma) and it is the jointly normalized data that are available here. The data are presented in the form of an exprSet object. 1

2 2 ALL Usage data(ALL) Format The different covariates are: cod : The patient IDs. • • diagnosis The date of diagnosis. The sex of the patient, coded as • and F . sex M age The age of the patient in years. • BT The type and stage of the disease; B indicates B-cell ALL while a • indicates T-cell ALL. T • A factor with two levels, either CR indicate that remission was achieved or REF remission indicating that the patient was refractory and remission was not achieved. • A vector with the following values: 1: “CR”, remission achieved; 2: “DEATH IN CR”, CR patient died while in remission; 3: “DEATH IN INDUCTION”, patient died while in induction therapy; 4: “REF”, patient was refractory to therapy. date.cr • The date on which remission was achieved. • t(4;11) A logical vector indicating whether a t(4;11) translocation was detected. • t(9;22) A logical vector indicating whether a t(9;22) translocation was detected. • cyto.normal A logical vector indicating whether the cytogenetics were normal. • citog A vector indicating the various cytogenetic abnormalities that were detected. mol.biol • The assigned molecular biology of the cancer (mainly for those with B-cell ALL), BCR\/ABL, ALL\/AF4, E2APBX etc. • fusion protein For those with BCR\/ABL which of the fusion proteins was detected, p190 , , p210 p190\/p210 . • The patients response to multidrug resistance, either NEG , or mdr . POS • kinet ploidy, either diploid or hyperd. • ccr A vector indicating whether the patient had continuous complete remission nor not. • relapse A vector indicating whether the patient had relapse or not. transplant Did the patient receive a bone marrow transplant or not. • f.u Follow-up data. The possible values are 1: “AUBMT \/ REL”: autologous bone marrow • transplant and subsequent relapse; 2: “BMT \/ CCR”: allogeneic bone marrow transplant and still in continuous complete remission; 3: “BMT \/ DEATH IN CR”: after allogeneic bone marrow transplant patient died without relapsing; 4: “BMT \/ REL”: after allogeneic bone marrow transplant patient relapsed; 5: “CCR”: patient was in continuous complete remission; 6: “CCR \/ OFF”: patient was in continuous complete remission but off-protocol for some reasons; 7: “DEATH IN CR”: died when in complete remission; 8: “MUD \/ DEATH IN CR”: unrelated allogeneic bone marrow transplant and death without relapsing; 9: “REL”: relapse; 10: “REL \/ SNC”: relapse occurred at central nervous system. • date last seen Date the patient was last seen. Source Sabina Chiaretti, Xiaochun Li, Robert Gentleman, Antonella Vitale, Marco Vignetti, Franco Man- delli, Jerome Ritz, and Robin Foa Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood, 1 April 2004, Vol. 103, No. 7.

3 tojulian 3 Examples data(ALL) tojulian Convert Calendar Date to Julian Time Description Convert Calendar Date in the form of "%m/%d/%Y" to Julian time, number of days since 1970-01- 01 in the time zone of "GMT". Usage tojulian(x) Arguments x Date to convert Author(s) Robert Gentleman Examples ds <- tojulian(c("4/8/2000", "4/30/2000")) ds[2]-ds[1]

4 Index Topic datasets ∗ ALL , 1 ∗ Topic programming tojulian , 3 ALL , 1 tojulian , 3 4

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