Package 'SMITIDstruct' reference manual

Title:	Data Structure and Manipulations Tool for Host and Viral Population
Description:	Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.
Authors:	Jean-Francois Rey [aut, cre]
Maintainer:	Jean-Francois Rey <[email protected]>
License:	GPL (>= 2) \| file LICENSE
Version:	0.0.5
Built:	2024-12-10 06:33:19 UTC
Source:	CRAN

Data Structure and Manipulation Tool for Host and Viral Population

Description

Statistical Methods for Inferring Transmissions of Infectious Diseases from deep sequencing data (SMITID). It allow sequence-space-time host and viral population data storage, indexation and querying.

Details

Package:	SMITIDstruct
Type:	Package
Version:	0.0.5
Date:	2019-06-14
License:	GPL (>=2)

The SMITIDstruct package contains functions and methods for manipulating Host and Viral population genotico-space-time data.

Author(s)

Jean-Francois Rey [email protected]

Maintainer: Jean-Francois Rey [email protected]

Examples


## Run a simulation
library("SMITIDstruct")
demo.SMITIDstruct.run() 


## Run a simulation
library("SMITIDstruct")
demo.SMITIDstruct.run()

addcode

Description

add a code event to an another

Usage

addcode(code, code.add)
addcode(code, code.add)

Arguments

`code`	an existing code
`code.add`	the code to add

Value

merge of the two code

addHost

Description

add an Host to a HostSet

Usage

addHost(lhost, id)
addHost(lhost, id)

Arguments

`lhost`	a hostSet Object
`id`	a character of host ID

Value

a HostSet of host object with there ID

Examples

lhost <- list()
lhost <- addHost(lhost,"42")

lhost <- list()
lhost <- addHost(lhost,"42")

addIndex

Description

add to an index a new eventcode

Usage

addIndex(index, id_host, time, code)
addIndex(index, id_host, time, code)

Arguments

`index`	an index
`id_host`	an host index in HostSet
`time`	a time
`code`	an event code

Value

the index updated (add a row or update one)

addViralObs

Description

load Viral pop observation in Host object

Usage

addViralObs(lhost, lvpop)
addViralObs(lhost, lvpop)

Arguments

`lhost`	a HostSet
`lvpop`	a ViralPopSet

Value

lhost update with viral population observed

alleleCount

Description

count allele at each position

Usage

alleleCount(mat, seq.char = c("A", "T", "G", "C"))
alleleCount(mat, seq.char = c("A", "T", "G", "C"))

Arguments

`mat`	a genomique seq list as matrix by row
`seq.char`	allele alphabet

Value

a matrix, each row as a unique seq and col as allele count by position

concatViralPop

Description

concat several Viral population in one ViralPop object

Usage

concatViralPop(lvpop, lid)
concatViralPop(lvpop, lid)

Arguments

`lvpop`	a ViralPop Set
`lid`	vector of viralpop id to concat

Value

a ViralPop object with ID concatenation from all IDs and time at 0.

createAViralPop

Description

Create a new ViralPop object

Usage

createAViralPop(host_id, obs_time, seq, id_seq = "seq_ID",
  seq_value = "seq", prop = "prop", compact = FALSE)
createAViralPop(host_id, obs_time, seq, id_seq = "seq_ID",
  seq_value = "seq", prop = "prop", compact = FALSE)

Arguments

`host_id`	host ID which viral pop is observed
`obs_time`	time of the observation (numeric or date)
`seq`	a data.frame of sequences ID, sequences and counts
`id_seq`	column name containing the sequences ID
`seq_value`	column name containing the sequences
`prop`	column name containing the count of each sequences
`compact`	boolean, default FALSE, if TRUE will try group identicals sequences (not implemented yet)

createHost

Description

create a list of Host class object

Usage

createHost(list_host)
createHost(list_host)

Arguments

list_host

a character vector of host ID

Value

a HostSet of host object with there ID

Examples

lh <- seq(1,30,1)
lhost <- createHost(lh)

lh <- seq(1,30,1)
lhost <- createHost(lh)

createIndex

Description

create an index of time id_host and event code

Usage

createIndex(hostlist)
createIndex(hostlist)

Arguments

hostlist

a Hostset

Value

a data.frame with TIME, ID_HOST and EVENTCODE as columns

demo.SMITIDstruct.run

Description

run a demo to load HostSet, ViralPopSet and index

Usage

demo.SMITIDstruct.run()
demo.SMITIDstruct.run()

diversity.pDistance

Description

diversity calculation using Mean Pairwise Distance

Usage

diversity.pDistance(vpop)
diversity.pDistance(vpop)

Arguments

vpop

a ViralPop object

Value

result

diversity.sfs

Description

Allele frequency spectrum or Site frequency spectra : the distribution of alternative allele frequencies across all sites of genetic sequences

Usage

diversity.sfs(vpop)
diversity.sfs(vpop)

Arguments

vpop

a viralPop class

Value

the site frequency spectra

getCov

Description

get Host(s) covariates

Usage

getCov(lhost, id = NA)
getCov(lhost, id = NA)

Arguments

`lhost`	a HostSet
`id`	a vector of host id (default NA : all lhost)

Value

a data.frame

getDate

Description

Converte timestamp to Date (string)

Usage

getDate(time, format = "%Y-%m-%dT%H:%M:%S")
getDate(time, format = "%Y-%m-%dT%H:%M:%S")

Arguments

`time`	a timestamp or vector of
`format`	Date format output (default %Y-%m-%dT%H:%M:%S)

Value

time as string date

getDiversity.pDistance

Description

get pairwise distance of an host over viral population observated

Usage

getDiversity.pDistance(host, lvpop)
getDiversity.pDistance(host, lvpop)

Arguments

`host`	an Host object
`lvpop`	a ViralPopSet object

Value

a data.frame with col as time of observation and p_distance

getDiversity.sfs

Description

get Allele Frequency Spectrum or Site Frequency spectra for observated viral pop of an host

Usage

getDiversity.sfs(host, lvpop)
getDiversity.sfs(host, lvpop)

Arguments

`host`	an Host object
`lvpop`	an ViralPopSet object

Value

a list indexed by time that contains allele.time and count

getInfosByHostAndTime

Description

get hosts informations, status, infectedby, coordinates and time

Usage

getInfosByHostAndTime(index, lhost)
getInfosByHostAndTime(index, lhost)

Arguments

`index`	an index
`lhost`	a hosts list

Value

a data.frame with colnames (id, time, infectedby, status, probabilities, X ,Y)

getStates

Description

get Host(s) states

Usage

getStates(lhost, id = NA)
getStates(lhost, id = NA)

Arguments

`lhost`	a HostSet
`id`	a vector of host id (default NA : all lhost)

Value

a data.frame

getTimeLine

Description

get the time line of an host

Usage

getTimeLine(lhost, id)
getTimeLine(lhost, id)

Arguments

`lhost`	a hostSet
`id`	a host ID

Value

a data.frame

getTimestamp

Description

Get the timestamp of Date

Usage

getTimestamp(date, format = "%Y-%m-%dT%H:%M:%S")
getTimestamp(date, format = "%Y-%m-%dT%H:%M:%S")

Arguments

`date`	a date (as string) or vector of
`format`	the date format (default %Y-%m-%dT%H:%M:%S)

Value

timestamp of the date(s)

getTransmissionTree

Description

get a transmission tree as a data.frame

Usage

getTransmissionTree(lhost, id = NA)
getTransmissionTree(lhost, id = NA)

Arguments

`lhost`	a hostSet
`id`	a vector of hosts ids (default NA : all host)

Value

a data.frame as source|target|time in columns

Examples

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))
print(getTransmissionTree(lhost))
path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))
print(getTransmissionTree(lhost))

Class Host

Description

Spatio-temporal information about Host.

Details

Object can be created by calling ...

rdname Host-class

Slots

ID: Host identifier
coordinates: Host coordinates in time (as sf)
states: Host States/Status (dob, Inf...)
sources: data.frame of time and host id who infected this host
offsprings: data.frame of time and host id who has been contamined by this host
ID_V_POP: data.frame of time and index of Viral population Observation
covariates: data.frame of time, cavariate and value of this host.

is.juliendate

Description

Chekc if a numeric is not a timestamp

Usage

is.juliendate(time)
is.juliendate(time)

Arguments

time

a numeric

Value

TRUE if time is a julien day, otherwise FALSE

is.StringDate

Description

Check if a string represent a date

Usage

is.StringDate(date)
is.StringDate(date)

Arguments

date

a string or a vector of string (without NA)

Value

TRUE if date contains date format

is.timestamp

Description

Check if a numeric represent a timestamp

Usage

is.timestamp(time)
is.timestamp(time)

Arguments

time

a numeric

Value

TRUE if time >= 1971

isInCode

Description

check a code contains a specific code

Usage

isInCode(code, thecode)
isInCode(code, thecode)

Arguments

`code`	list of code to test
`thecode`	the real code

Value

TRUE if code contain thecode otherwise FLASE

loadCoords

Description

Load Hosts states

Usage

loadCoords(lhost, dfCoords, id = "ID")
loadCoords(lhost, dfCoords, id = "ID")

Arguments

`lhost`	a HostSet
`dfCoords`	a data.frame with host ID, time and longitude latitude values
`id`	colname for host ID

Value

lhost updated

Examples

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))
coords <- read.table(file=paste(path,"/hosts_coords.txt",sep=''), header=TRUE, check.names=FALSE)
lhost <- loadCoords(lhost,coords)
path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))
coords <- read.table(file=paste(path,"/hosts_coords.txt",sep=''), header=TRUE, check.names=FALSE)
lhost <- loadCoords(lhost,coords)

loadCovs

Description

Load Hosts covariates

Usage

loadCovs(lhost, dfCovs, id = "ID", colCovs)
loadCovs(lhost, dfCovs, id = "ID", colCovs)

Arguments

`lhost`	a HostSet
`dfCovs`	a data.frame with host ID in rows and covariates in columns
`id`	colname for host ID
`colCovs`	colnames of covariates columns

Value

lhost updated with covariates

loadHost

Description

load host object from a file

Usage

loadHost(file = "host.txt")
loadHost(file = "host.txt")

Arguments

file

a file containing hosts data

Value

a list of Host object (HostSet) include Class-Host.R

loadStates

Description

Load Hosts states

Usage

loadStates(lhost, dfStates, id = "ID", colStates)
loadStates(lhost, dfStates, id = "ID", colStates)

Arguments

`lhost`	a HostSet
`dfStates`	a data.frame with host ID and states in columns and time as value
`id`	colname for host ID
`colStates`	colnames of States columns

Value

lhost updated

Examples

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
class(lhost) <- "hostSet"
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep='')) 
obs <- read.table(paste(path,"/obs.txt",sep=''),header=TRUE, check.names=FALSE)
obs.states <- c(colnames(obs[-grep("ID|Tobs.*",colnames(obs))]))
lhost <- loadStates(lhost, obs, colStates=obs.states)
path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
class(lhost) <- "hostSet"
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep='')) 
obs <- read.table(paste(path,"/obs.txt",sep=''),header=TRUE, check.names=FALSE)
obs.states <- c(colnames(obs[-grep("ID|Tobs.*",colnames(obs))]))
lhost <- loadStates(lhost, obs, colStates=obs.states)

loadTree

Description

load sources and offsprings from file

Usage

loadTree(lhost = list(), file = "tree.txt", source = "ID-source",
  receptor = "ID-receptor", tinf = "Tinf", weight = "Weight")
loadTree(lhost = list(), file = "tree.txt", source = "ID-source",
  receptor = "ID-receptor", tinf = "Tinf", weight = "Weight")

Arguments

`lhost`	a HostSet
`file`	a file containing tree data
`source`	column name for source ID
`receptor`	column name for receptor ID
`tinf`	column name for infection Time
`weight`	column name of infection weight

Value

the lhost param update with sources and offsprings

Examples

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
class(lhost) <- "hostSet"
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))
path = system.file("extdata", "data-simul/", package="SMITIDstruct")
lhost <- list()
class(lhost) <- "hostSet"
lhost <- loadTree(lhost,paste(path,"/tree.txt",sep=''))

loadTreeDF

Description

load sources and offsprings from a data.frame

Usage

loadTreeDF(lhost = list(), df = data.frame(), source = "ID-source",
  receptor = "ID-receptor", tinf = "Tinf", weight = "Weight")
loadTreeDF(lhost = list(), df = data.frame(), source = "ID-source",
  receptor = "ID-receptor", tinf = "Tinf", weight = "Weight")

Arguments

`lhost`	a HostSet
`df`	a data.frame containing tree data
`source`	column name for source ID
`receptor`	column name for receptor ID
`tinf`	column name for infection Time
`weight`	infection links probability

Value

the lhost param update with sources and offsprings

loadViralObs

Description

load a ViralPop object

Usage

loadViralObs(id, time, file)
loadViralObs(id, time, file)

Arguments

`id`	host pathogen ID
`time`	time of the observation (numeric or Date)
`file`	a fasta file

Value

a new ViralPop object

loadViralPop

Description

Load all ViralPop observated in the file.obs

Usage

loadViralPop(directory, listFiles, listCol = list(id = "id", timeObs =
  "time", filename = "filename"), file.extension = "fasta")
loadViralPop(directory, listFiles, listCol = list(id = "id", timeObs =
  "time", filename = "filename"), file.extension = "fasta")

Arguments

`directory`	path where is data
`listFiles`	a dataframe with host ID, time observation and file name (filename.fasta)
`listCol`	a list of listFiles colomns names ("id", "timeObs", "filename")
`file.extension`	genotype file extension

Value

a vector of VirlaPop object

Examples


path = system.file("extdata", "data-simul/", package="SMITIDstruct")
files <- list.files(path, pattern = ".*.fasta" ,full.names=FALSE)
lfileinfo <- sapply(files,function(x){return(substr(x,1,nchar(x)-6))})
splitFiles <- strsplit(lfileinfo, "_");
listF <- cbind(data.frame(matrix(unlist(splitFiles),nrow=length(splitFiles), byrow=TRUE),
               stringsAsFactors = FALSE), names(splitFiles))
colnames(listF) <- c("id", "time", "filename")
lvpop <- loadViralPop(path,listF)

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
files <- list.files(path, pattern = ".*.fasta" ,full.names=FALSE)
lfileinfo <- sapply(files,function(x){return(substr(x,1,nchar(x)-6))})
splitFiles <- strsplit(lfileinfo, "_");
listF <- cbind(data.frame(matrix(unlist(splitFiles),nrow=length(splitFiles), byrow=TRUE),
               stringsAsFactors = FALSE), names(splitFiles))
colnames(listF) <- c("id", "time", "filename")
lvpop <- loadViralPop(path,listF)

loadViralPopSet

Description

load a list of viral populations

Usage

loadViralPopSet(lvpop = list(), list)
loadViralPopSet(lvpop = list(), list)

Arguments

`lvpop`	a viralPopSet (default new one)
`list`	a list (see details)

Details

The list have to be on this format: list$HOST_ID$TIME$list$seq_id $seq $prop A list indexed by host ID, follow by a list indexed by time (of observation). The last list contains an array of seq_ID (sequence ID), an array of seq (sequence as characters), and an array of the count of seq. example : $'HOST_42'$'2014-01-01T00:00:00'$seq_ID ["SEQ_1","SEQ_2"] $'HOST_42'$'2014-01-01T00:00:00'$seq ["ACGT","TGCA"] $'HOST_42'$'2014-01-01T00:00:00'$seq_ID ["46","6"]

mergeCode

Description

merge a list of event code

Usage

mergeCode(listcode)
mergeCode(listcode)

Arguments

listcode

a list of event code*

Value

a code

plotDiversity.pDistance

Description

plot Mean Pairwise Distance for an host viralpop over time

Usage

plotDiversity.pDistance(host, lvpop)
plotDiversity.pDistance(host, lvpop)

Arguments

`host`	an Host object
`lvpop`	a ViralPopSet object

plotDiversity.sfs

Description

plot Allele frequency spetrum for an host viralpop over time

Usage

plotDiversity.sfs(host, lvpop)
plotDiversity.sfs(host, lvpop)

Arguments

`host`	an Host object
`lvpop`	an ViralPopSet object

setStates

Description

set hosts states from a data.frame

Usage

setStates(lhost, dfStates, colStates = c(id = "ID", time = "time", states
  = "value"))
setStates(lhost, dfStates, colStates = c(id = "ID", time = "time", states
  = "value"))

Arguments

`lhost`	a HostSet
`dfStates`	a data.frame with host ID and states and time in columns
`colStates`	vector of the columns name, id, time and states

Value

the HostSet updated

simulateStates

Description

simulate states from sources infection

Usage

simulateStates(lhost)
simulateStates(lhost)

Arguments

lhost

a HostSet

Value

lhost update with states from sources time ~

Class ViralPop

Description

Viral population data containing genotypes

Slots

ID: Host identifier
time: Observation time as numeric since 1970/01/01
size: Qt of variants
names: list of variants id with same sequence
genotypes: all variants genotypes (as DNAStringSet)
proportions: proportions of each variants

Package 'SMITIDstruct'

Help Index

Data Structure and Manipulation Tool for Host and Viral Population

Description

Details

Author(s)

See Also

Examples

addcode

Description

Usage

Arguments

Value

addHost

Description

Usage

Arguments

Value

Examples

addIndex

Description

Usage

Arguments

Value

addViralObs

Description

Usage

Arguments

Value

alleleCount

Description

Usage

Arguments

Value

concatViralPop

Description

Usage

Arguments

Value

createAViralPop

Description

Usage

Arguments

createHost

Description

Usage

Arguments

Value

Examples

createIndex

Description

Usage

Arguments

Value

demo.SMITIDstruct.run

Description

Usage

diversity.pDistance

Description

Usage

Arguments

Value

diversity.sfs

Description

Usage

Arguments

Value

getCov

Description

Usage

Arguments

Value

getDate

Description

Usage

Arguments

Value

getDiversity.pDistance

Description

Usage