Package 'msd16s'

Curated dataset of many healthy and moderate-to-severe diarretic gut 16s samples on the 454 FLEX platform.

Description

Data used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. Measurements are number of reads clustered into OTUs (operatonal taxanomic units) by DNAClust.

Author(s)

Joseph N. Paulson

References

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.

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Curated dataset of many healthy and moderate-to-severe diarretic gut 16s samples on the 454 FLEX platform.

Description

Data used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. Measurements are number of reads annotated for a particular cluster within a given sample followed by filtering. Sequencing was performed on the 454 Flex platform.

format

Data is stored as an MRexperiment-class object. Using MRcounts one can obtain the 16S count matrix produced using using DNAclust (http://dnaclust.sourceforge.net/). The pData function accesses a data frame with the following columns:

Type:

Status of samples: Case, Control

Country:

Country of origin

Age:

Month

AgeFactor:

Month group

Dysentery:

Dysentteric (1) non-dysenterric (0) indicator

The fData function accesses a data frame with the following columns:

OTU:

OTU cluster id

Taxonomy:

Full taxonomic profile

superkingdom:

superkingdom

phylum:

phylum

class:

class

order:

order

family:

family

genus:

genus

species:

species

clusterCenter:

The OTU cluster's representative sequence

Author(s)

Joseph N. Paulson

References

'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'

See Also

MRexperiment-class for the class definition, cumNorm to normalize the counts.

Examples

data(msd16s)
head(pData(msd16s))
head(fData(msd16s))

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