MIGSAres-common {MIGSA} | R Documentation

## MIGSAres exploratory functions

### Description

Several R base overwritten functions to manipulate a MIGSAres object as a data.frame way. NOTE: When subsetting a MIGSAres object, if it does not have the id, GS_Name and (at least) one experiment columns, then it wont be a MIGSAres object, i.e., migsaRes[,c("id","igsaInput1")] is no longer a MIGSAres object.

### Usage

    ## S4 method for signature 'MIGSAres'
    dim(x)

    ## S4 method for signature 'MIGSAres'
    x$name

    ## S4 method for signature 'MIGSAres'
    colnames(x)

    ## S4 method for signature 'MIGSAres'
    head(x, n = 6L)

    ## S4 method for signature 'MIGSAres'
    tail(x, n = 6L)

    ## S4 method for signature 'MIGSAres,ANY,ANY,ANY'
    x[i, j, drop = FALSE]

    ## S4 method for signature 'MIGSAres'
    show(object)

    ## S4 method for signature 'MIGSAres'
    as.data.frame(x)

    ## S4 method for signature 'MIGSAres,MIGSAres'
    merge(x, y)

### Arguments

`x` | MIGSAres object.
`name` | as used in `$`.
`n` | as used in `head` and `tail`.
`i` | as used in `[`.
`j` | as used in `[`.
`drop` | as used in `[` (default: FALSE).
`object` | MIGSAres object.
`y` | MIGSAres object.

### Value

Desired object.

### Examples

    data(migsaRes);
    ## As we ran MIGSA for two experiments and 200 gene sets, it must have 200
    ## rows, and five columns (id, Name, GS_Name, and the experiments names).
    dim(migsaRes);

    ## migsaRes shown as data.frame has these column names: id, Name, GS_Name,
    ## and the experiments names. As we ran two experiments, names igsaInput1
    ## and igsaInput2, we can use $ in these ways:
    head(migsaRes$id);
    table(migsaRes$Name);
    table(migsaRes$GS_Name);
    head(migsaRes$igsaInput1);
    head(migsaRes$igsaInput2);

    colnames(migsaRes);

    head(migsaRes);

    ## Or see the first 10
    head(migsaRes, n=10);

    tail(migsaRes);

    ## Or see the last 10
    tail(migsaRes, n=10);

    ## migsaRes shown as data.frame has these column names: id, Name, GS_Name,
    ## and the experiments names. As we ran two experiments, names igsaInput1
    ## and igsaInput2, we can use [ in these ways:

    ## Lets get the first 5 rows and 4 columns (the result is a MIGSAres object).
    migsaRes[1:5, 1:4];
    class(migsaRes[1:5, 1:4]);

    ## Lets get the experiments results. Note that this is not any more a
    ## MIGSAres object.
    migsaRes[, c("igsaInput1", "igsaInput2")];
    class(migsaRes[, c("igsaInput1", "igsaInput2")]);

    migsaRes;

    migsaResDFrame <- as.data.frame(migsaRes);
    head(migsaResDFrame);

    migsaRes1 <- migsaRes[,1:4];
    migsaRes2 <- migsaRes[,c(1:3,5)];
    migsaResMerged <- merge(migsaRes1, migsaRes2);

[Package MIGSA version 1.8.1 Index]