vignettes/MetNormalizer.Rmd
MetNormalizer.RmdYou can install MetNormalizer from Github.
# Install `MetNormalizer` from GitHub
if(!require(devtools)){
install.packages("devtools")
}
devtools::install_github("jaspershen/MetNormalizer")We use the demo data in demoData package to show how to use MetNormalizer. Please install it first.
devtools::install_github("jaspershen/demoData")
library(demoData)
library(MetNormalizer)
path <- system.file("MetNormalizer", package = "demoData")
file.copy(from = path, to = ".", overwrite = TRUE, recursive = TRUE)
#> [1] TRUE
new.path <- file.path("./MetNormalizer")MetNormalizer
metNor(
ms1.data.name = "data.csv",
sample.info.name = "sample.info.csv",
minfrac.qc = 0,
minfrac.sample = 0,
optimization = TRUE,
multiple = 5,
threads = 4,
path = new.path
)
#> Checking data...
#> Read data.
#> --------------------------------------------------------------
#> There are 177 samples in your data.
#> --------------------------------------------------------------
#> --------------------------------------------------------------
#> Summary:
#> Check result OK Warning Error
#> data Valid 7 0 0
#> sample.info Valid 8 0 0
#>
#>
#> data:
#> data is valid.
#>
#> sample.info:
#> sample.info is valid.
#> Reading data...
#> Filtering data...
#> OK
#> SVR normalization...
#>
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#> SVR normalization is done
#> All done!All the results will be placed in the folder named as svr_normalization_result.