lineup (version 0.44)

subset.lineupdist: 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 lineupdist
subset(x, rows = NULL, cols = NULL, ...)
# S3 method for lineupdist
[(x, rows = NULL, cols = NULL)

Value

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

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.

Author

Karl W Broman,

See Also

disteg(), distee(), pulldiag()

Examples

data(expr1, expr2)
expr1 <- expr1[,1:100]; expr2 <- expr2[,1:100]

# 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]