getCmatrix {safe}R Documentation

Generation of a C matrix

Description

This function will convert a list, vector or file of gene annotation into a C matrix. Size constraints, and present/absent calls can be set to filter categories and genes accordingly.

Usage

  getCmatrix(keyword.list, present.genes=, GO.ont=)
  getCmatrix(gene.list, present.genes=, min.size=, max.size=)
  getCmatrix(vector=, delimiter=, as.matrix=)
  getCmatrix(file=, delimiter=, ...)

Arguments

keyword.list A list containing character vectors for each keyword that specify the gene members.
gene.list A list containing character vectors for each gene that specify the functional categories it belongs to.
vector A character vector of gene annotation with a specified delimiter between category keywords.
file A file containing the character vector of gene annotation.
delimiter Delimiter used between category keywords when provided as a vector or file.
present.genes An optional vector used to filter genes in the C matrix. Can be provided as an unordered character vector of gene names that match names(list), or as an ordered vector of presence (1) and absence (0) calls.
GO.ont "CC","BP",or "MF" specify the ontology to limit categories to.
min.size Optional minimum category size to be considered.
max.size Optional maximum category size to be considered.
as.matrix Optional argument to specify a matrix is returned rather than a matrix.csr.
... Any extra arguments will be forwarded to the read.table function when category assignments are given as a file.

Value

C.mat.csr If as.matrix=F a sparse matrix is returned with the rows corresponding to the genes and columns are categories
row.names Character vector of gene names
col.names Character vector of category names

Author(s)

William T. Barry: bill.barry@duke.edu

References

W. T. Barry, A. B. Nobel and F.A. Wright, 2005, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics {bf 21}(9) 1943-9.

See also the vignette included with this package.

See Also

{safe, safeplot, getPImatrix,.}

Examples

## A simple illustration
anno <- c("Keyword1","Keyword2;Keyword3","",
          "Keyword3;Keyword1","Keyword3")
names(anno) <- paste("Gene",1:5)

getCmatrix(vector = anno, delimiter = ";",
           as.matrix=TRUE)

[Package safe version 2.2.0 Index]