Description Usage Arguments Details Value Author(s) Examples
View source: R/cbaf-automatedStatistics.R
This function calculates frequency percentage, frequency ratio, mean value and median value of samples greather than specific cutoff in the selected study / subgroups of the study. Furthermore, it can looks for the five genes that contain the highest values in each study / study subgroup. It uses the data generated by obtainOneStudy()/obtainMultipleStudies() function.
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a character string containing name of interest. It is used for naming the process.
a character string that specifies the type of input
data produced by the previous function. Two options are availabe:
a character vector that containes the statistical procedures
users prefer the function to compute. The complete results can be obtained
a logical value that, if set as TRUE, causes the function to
create three data.frame that contain the five top genes for each cancer. To
get all the three data.frames, "frequencyPercentage", "meanValue" and
"MedianValue" must have been included for
a number used to limit samples to those that are greather than
this number (cutoff). The default value for methylation data is
a logical value that, if set to be
A new section in the BiocFileCache object that was created by one of
the obtainOneStudy() or obtainMultipleStudies() functions. It contains a list
that contains some or all of the following statistical measurements for
every gene group, based on what user has chosen:
Arman Shahrisa, email@example.com [maintainer, copyright holder]
Maryam Tahmasebi Birgani, firstname.lastname@example.org
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genes <- list(K.demethylases = c("KDM1A", "KDM1B", "KDM2A", "KDM2B", "KDM3A", "KDM3B", "JMJD1C", "KDM4A"), K.methyltransferases = c("SUV39H1", "SUV39H2", "EHMT1", "EHMT2", "SETDB1", "SETDB2", "KMT2A", "KMT2A")) obtainOneStudy(genes, "test", "Breast Invasive Carcinoma (TCGA, Cell 2015)", "RNA-Seq", desiredCaseList = c(3,4)) automatedStatistics("test", obtainedDataType = "single study", calculate = c("frequencyPercentage", "frequencyRatio"))
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