get.data: Parsing the data file.

Description Usage Author(s) References Examples

View source: R/get.data.R

Description

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:

1
2
3
4
5
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)	...

In the latest version 1.1 you will be able to load your data as BIOM format, just adding the "Class" information in the second row as follows:

1
2
3
4
5
6
7
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)	...

Usage

1

Author(s)

Alfonso Benitez-Paez

References

Benitez-Paez A. & Sanz Y. (2015). Permubiome: an R package to perform permutation based test for biomarker discovery in microbiome analyses. In press.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
## The function is currently defined as
function () 
{
    DATA <- readline("Type the name of your data set : ")
    if (DATA == "") {
        tb <- read.table(system.file("extdat", "DATA_1", package = "permubiome"), 
            header = T, sep = "\t")
        print(paste("As you declare no input file, the permubiome test data was loaded"))
        save(tb, file = "permubiome.RData")
    }
    else {
        FORMAT <- readline("Type the format of your data set (PERMUBIOME or BIOM): ")
        if (FORMAT == "PERMUBIOME") {
            tb <- read.table(DATA, header = T, sep = "\t")
            save(tb, 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")
        }
    }
    load("permubiome.RData")
    df <- as.data.frame(tb)
    classes <- levels(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(df, file = "permubiome.RData")
  }

permubiome documentation built on May 29, 2017, 11:27 a.m.