genefinder {genefilter} | R Documentation |

## Finds genes that have similar patterns of expression.

### Description

Given an `exprSet`

or a matrix of gene expressions, and the
indices of the genes of
interest, `genefinder`

returns a list of the
`numbResults`

closest genes.
The user can specify one of the standard distance measures listed
below.
The number of values to return can be specified. The return value is a
list with two components:
genes (measured through the desired distance method) to the genes
of interest (where X is the number of desired results returned) and
their distances.

### Usage

genefinder(X, ilist, numResults=25, scale="none", weights, method="euclidean")

### Arguments

`X` |
A numeric matrix where columns represent patients, and rows
represent genes. |

`ilist` |
Vector of genes of interest. Contains indices of genes
in matrix X. |

`numResults` |
Number of results to display, starting from the least
distance to the greatest. |

`scale` |
one of 'none', 'range', or 'zscore'. Scaling
is carried out separately on each row. |

`weights` |
A vector of weights applied across the columns of
`X` . If no weights are supplied, no weights are applied |

`method` |
one of "euclidean", "maximum", "manhattan", "canberra",
"correlation", "binary". |

### Details

If the scale option is "range", then the input matrix is scaled using
genescale(). If it is "zscore", then the input matrix is scaled using
the 'scale' builtin with no arguments.

The method option specifies the metric used for gene comparisons. The
metric is applied, row by row, for each gene specified in `ilist`

.

The "correlation" option for the distance method will return a value
equal to 1-correlation(x).

See `dist`

for a more detailed description of the distances.

### Value

The returned value is a list containing an entry for each gene
specified in ilist. Each list entry contains an array of distances
for that gene of interest.

### Author(s)

J. Gentry and M. Kajen

### See Also

`genescale`

### Examples

set.seed(12345)
#create some fake expression profiles
m1 <- matrix (1:12, 4, 3)
v1 <- 1
nr <- 2
#find the 2 rows of m1 that are closest to row 1
genefinder (m1, v1, nr, method="euc")
v2 <- c(1,3)
genefinder (m1, v2, nr)
genefinder (m1, v2, nr, scale="range")
genefinder (m1, v2, nr, method="manhattan")
m2 <- matrix (rnorm(100), 10, 10)
v3 <- c(2, 5, 6, 8)
nr2 <- 6
genefinder (m2, v3, nr2, scale="zscore")

[Package

*genefilter* version 1.8.0

Index]