MIGSAres-common: MIGSAres exploratory functions

In MIGSA: Massive and Integrative Gene Set Analysis

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)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.