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

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);