subset.lineupdist: Subsetting distance matrix

In kbroman/lineup: Lining Up Two Sets of Measurements

Subsetting distance matrix

Description

Pull out a specified set of rows and columns from a distance matrix calculated by distee() or disteg().

Usage

## S3 method for class 'lineupdist'
subset(x, rows = NULL, cols = NULL, ...)

## S3 method for class 'lineupdist'
x[rows = NULL, cols = NULL]

Arguments

x	A distance matrix object as obtained from distee() or disteg().
rows	Optional vector of selected rows.
cols	Optional vector of selected columns.
...	Ignored at this point.

Value

The input distance matrix object, but with only the specified subset of the data.

Author(s)

Karl W Broman, [e-mail]

See Also

disteg(), distee(), pulldiag()

Examples

data(expr1, expr2)


# find samples in common
id <- findCommonID(expr1, expr2)

# calculate correlations between cols of x and cols of y
thecor <- corbetw2mat(expr1[id$first,], expr2[id$second,])

expr1s <- expr1[,thecor > 0.8]/1000
expr2s <- expr2[,thecor > 0.8]/1000

# calculate correlations among samples
d <- distee(expr1s, expr2s, d.method="cor")

# pull out distances for samples 24, 92, 44, 66
samp <- c("24", "92", "44", "66")
d[samp, samp]

kbroman/lineup documentation built on July 19, 2024, 8:22 p.m.