View source: R/get.data.R View source: R/get.data_OPT.R
get.data | R Documentation |
This function prompts for the file contained all the data needed to process. You only have to execute this function in the working directory where your file is stored properly formatted as requested.
The input file is a tab-delimited text matrix as follows:
Sample Class feature(1) feature(2) feature(n) ... sampleA classX counts(A1) counts(A2) counts(An) ... sampleB classY counts(B1) counts(B2) counts(Bn) ... sampleC classX counts(C1) counts(C2) counts(Cn) ... sampleD classY counts(D1) counts(D2) counts(Dn) ...
From the version 1.1 on you will be able to load your data as COLUMN format, just adding the "Class" information in the second row as follows:
Sample sampleA sampleB sampleC sampleD ... Class classX classY classX classY ... feature(1) counts(A1) counts(B1) counts(C1) counts(D1) ... feature(2) counts(A2) counts(B2) counts(C2) counts(D2) ... feature(3) counts(A3) counts(B3) counts(C3) counts(D3) ... feature(4) counts(A4) counts(B4) counts(C4) counts(D4) ... feature(n) counts(An) counts(Bn) counts(Cn) counts(Dn) ...
get.data()
Alfonso Benitez-Paez
Benitez-Paez A. 2023. Permubiome: an R package to perform permutation based test for biomarker discovery in microbiome analyses. [https://cran.r-project.org]. Benitez-Paez A, et al. mSystems. 2020;5:e00857-19. doi: 10.1128/mSystems.00857-19.
## The function is currently defined as
function ()
{
DATA <- readline("Type the name of your data set : ")
if (substr(DATA, 1, 1) == ""){
tb <- read.table(system.file("extdat", "DATA_2", package = "permubiome"),
header = T, sep = "\t")
print(paste("As you declare no input file, the permubiome test data was loaded"))
save(tb, DATA, file = "permubiome.RData")
}
else {
FORMAT <- readline("Type the format of your data set (PERMUBIOME or COLUMN): ")
if (FORMAT == "PERMUBIOME") {
tb <- read.table(DATA, header = T, sep = "\t")
save(tb, FORMAT, file = "permubiome.RData")
}
else {
biom <- read.table(DATA, sep = "\t")
tb <- t(biom)
colnames(tb) <- tb[1, ]
rownames(tb) <- NULL
tb = tb[-1, ]
labels <- colnames(tb)
tb <- as.data.frame(tb)
for (i in 3:length(labels)) {
tb[, i] <- as.numeric(as.character(tb[, i]))
}
save(tb, file = "permubiome.RData")
}
}
print("opening DATA")
(load("permubiome.RData"))
df <- as.data.frame(tb)
classes <- levels(as.factor(df$Class))
samples <- nrow(df)
print(paste("Your data file contains:", samples, "samples"))
print(paste("The classes in your data file are:", classes[1],
"and", classes[2]))
print(paste("The number of different categories to compare are:",
(ncol(tb) - 2)))
save(tb, FORMAT, DATA, df, REFERENCE, classes, file = "permubiome.RData")
}
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