ecoli.data: Escherichia coli data

In ecolitk: Meta-data and tools for E. coli

Description

Meta-data related to Escherichia coli

Usage

data(ecoli.m52.genome)
data(ecoligenomeCHRLOC)
data(ecoligenomeSYMBOL2AFFY)
data(ecoligenomeSYMBOL)
data(ecoligenomeSTRAND)
data(ecoligenome.operon)
ecoli.len

Format

The format for ecoli.m52.genome is character with genome sequence. The format for ecoligenomeCHRLOC is an environment (as a hash table). Each key is an Affyemtrix probe set ID, and each value is vector of two integers (begining and end - see the details below) The format for ecoligenomeSYMBOL2AFFFY is an environment (as a hash table). Each key is a gene symbol name. The format for ecoligenomeSYMBOL is an environment (as a hash table). Each key is an Affymetrix probe set id ecoli.len is a variable containing the size of the genome in ecoli.m52.genome.

Details

The environments ecoligenomeSYMBOL2AFFFY and ecoligenomeSYMBOL are like the ones in the data packages built by annBuilder.

The environment ecoligenomeCHRLOC differs: two integers are associated with each key, one corresponds to the begining of the segment the other to the end.

The environment ecoligenomeSTRAND returns a logical. TRUE means that the orientation is ‘+’, FALSE means that the orientation is '-' (and NA is used when irrelevant for the key).

Source

http://www.genome.wisc.edu/sequencing/k12.htm and http://www.biostat.harvard.edu/complab/dchip/info_file.htm

Examples

data(ecoli.m52.genome)

ecolitk documentation built on Nov. 8, 2020, 5:29 p.m.