Description Usage Arguments Value Author(s) References Examples
When multiple probesets share the same gene symbols, select only the best probeset in terms of IQR
1 | DropDupGenes(dat, isParallel=FALSE, nCores=NULL, na.rm=TRUE)
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dat |
A gene expression matrix which has genes in rows and samples in columns. |
isParallel |
Whether to use multiple cores in parallel for fast computing. By default, it is false. |
nCores |
When isParallel is true, the number of cores can be set. By default, all cores in the machine are used in the unix-like machine, and 3 cores are used in windows. |
na.rm |
Whether to remove genes which have no annotation. Default is TRUE. |
A gene expression matrix which has unique genes in rows and samples in columns.
Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
Dongwan D. Kang and George C. Tseng. (2011) Meta-PCA: Meta-analysis in the Dimension Reduction of Genomic data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## Not run:
#One of example that shows how to generate a expression matrix used in the analysis
requireAll(c('GEOquery', 'affy', 'hgu133plus2.db'))
#It might be needed to download the source files first, and save it to local directory
#such as "./data/Prostate/Varambally" in this example
#ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE3325/GSE3325_series_matrix.txt.gz
Varambally <- getGEO('GSE3325', destdir="./data/Prostate/Varambally")
Varambally <- Varambally[[1]]
Varambally.sLabel <- as.character(pData(Varambally)$title)
Varambally.sLabel[grep("Benign",Varambally.sLabel)] <- "Normal"
Varambally.sLabel[grep("primary",Varambally.sLabel)] <- "Primary"
Varambally.sLabel[grep("Metastatic",Varambally.sLabel)] <- "Metastasis"
Varambally <- exprs(Varambally)
colnames(Varambally) <- Varambally.sLabel
rownames(Varambally) <- unlist(mget(rownames(Varambally), hgu133plus2SYMBOL))
Varambally <- DropDupGenes(Varambally, na.rm=TRUE)
Varambally <- log2(Varambally)
## End(Not run)
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