getCmatrix {safe} | R Documentation |
This function will convert a text file, vector or list of gene annotation into a C matrix. Size constraints, and present/absent calls can be set to filter categories and genes accordingly.
getCmatrix(list, present.genes=, min.size=, max.size=) getCmatrix(vector=, delimiter=) getCmatrix(file=, delimiter=, ...)
list |
A list containing character vectors for each gene that specify the functional categories it belongs to by keywords. |
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. |
min.size |
Optional minimum category size to be considered. |
max.size |
Optional maximum category size to be considered. |
... |
Any extra arguments will be forwarded to the read.table function when category assigments are given as a file. |
A matrix is returned with the rows corresponding to the genes as labeled by
names(list)
and each column corresponding to a category.
William T. Barry: wbarry@bios.unc.edu
W. T. Barry, A. B. Nobel and F.A. Wright, 2004, Significance Analysis of functional categories in gene expression studies: a structured permutation approach, Bioinformatics In press.
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 = ";")