micropan (version 1.0)

Mpneumoniae: Data sets for the Mycoplasma pneumoniae casestudy

Description

This data set contains several files with various objects related to the casestudy example used for illustration purposes in the micropan package.

Usage

data(Mpneumoniae.table)
data(Mpneumoniae.blast.distances)
data(Mpneumoniae.blast.clustering)
data(Mpneumoniae.blast.panmat)
data(Mpneumoniae.domain.clustering)
data(Mpneumoniae.domain.panmat)

Format

Mpneumoniae.table is a data.frame with 7 rows holding some information about the 7 genomes in the casestudy. Mpneumoniae.blast.distances is a data.frame with 3 columns holding all computed BLAST distances between pairs of sequences in the 7 genomes. This data.frame has 139 543 rows. Mpneumoniae.blast.clustering is a clustering vector of all the 9573 sequences in the genomes based on Mpneumoniae.blast.distances. Mpneumoniae.blast.panmat is a Panmat object containing a pan-matrix with 7 rows and 1210 columns based on Mpneumoniae.blast.clustering. Mpneumoniae.domain.clustering is a clustering vector of 5265 sequences in the genomes based on domain sequences. Notice that only sequences having at least one protein domain is considered here (5265 out of the total 9573). Mpneumoniae.domain.panmat is a Panmat object containing a pan-matrix with 7 rows and 445 columns based on Mpneumoniae.domain.clustering.

Examples

# Genome overview table
data(Mpneumoniae.table) #loads the Mpneumoniae.table
if(interactive()){
  View(Mpneumoniae.table)
} else {
  str(Mpneumoniae.table)
}

# BLAST distances, only the first 20 are displayed
data(Mpneumoniae.blast.distances) #loads the Mpneumoniae.blast.distances
if(interactive()){
  View(Mpneumoniae.blast.distances[1:20,])
} else {
  str(Mpneumoniae.blast.distances[1:20,])
}

# BLAST clustering vector
data(Mpneumoniae.blast.clustering) #loads the Mpneumoniae.blast.clustering
Mpneumoniae.blast.clustering[1:30]

# BLAST pan-matrix
data(Mpneumoniae.blast.panmat) #loads the Mpneumoniae.blast.panmat
summary(Mpneumoniae.blast.panmat)

# Domain sequence clustering vector
data(Mpneumoniae.domain.clustering) #loads the Mpneumoniae.domain.clustering
Mpneumoniae.domain.clustering[1:30]

# Domain sequence pan-matrix
data(Mpneumoniae.domain.panmat) #loads the Mpneumoniae.domain.panmat
summary(Mpneumoniae.domain.panmat)