getCmatrix {safe} | R Documentation |
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.
getCmatrix(keyword.list, present.genes=, GO.ont=) getCmatrix(gene.list, present.genes=, min.size=, max.size=) getCmatrix(vector=, delimiter=, as.matrix=) getCmatrix(file=, delimiter=, ...)
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. |
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 |
William T. Barry: bill.barry@duke.edu
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.
{safe
, safeplot
,
getPImatrix
,.}
## A simple illustration anno <- c("Keyword1","Keyword2;Keyword3","", "Keyword3;Keyword1","Keyword3") names(anno) <- paste("Gene",1:5) getCmatrix(vector = anno, delimiter = ";", as.matrix=TRUE)