Package 'OncoScore'

Title:	A tool to identify potentially oncogenic genes
Description:	OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.
Authors:	Luca De Sano [cre, aut] , Carlo Gambacorti Passerini [ctb], Rocco Piazza [ctb], Daniele Ramazzotti [aut] , Roberta Spinelli [ctb]
Maintainer:	Luca De Sano <[email protected]>
License:	file LICENSE
Version:	1.35.0
Built:	2024-10-30 08:29:50 UTC
Source:	https://github.com/bioc/OncoScore

Help Index

combine.query.results

Description

Merge a set of genes in a unique one in order to account for possible aliases

Usage

combine.query.results(query, genes, new.name)
combine.query.results(query, genes, new.name)

Arguments

`query`	The result of perform.query, perform.query.timeseries of perform.query.from.region
`genes`	A list of genes to be merged
`new.name`	A string containing the new name to be used for the new genes

Value

The frequencies of the genes in the cancer related documents and in all the documents retireved on PubMed

Examples

data(query)
combine.query.results(query, c('IDH1', 'IDH2'), 'new_gene')

data(query)
combine.query.results(query, c('IDH1', 'IDH2'), 'new_gene')

combine.single.matrix

Description

Perform merge procedure on a matrix

Usage

combine.single.matrix(query, genes, new.name)
combine.single.matrix(query, genes, new.name)

Arguments

`query`	The result of perform.query, perform.query.timeseries of perform.query.from.region
`genes`	A list of genes to be merged
`new.name`	A string containing the new name to be used for the new genes

Value

a merged matrix

compute.frequencies.scores

Description

compute the logaritmic scores based on the frequencies of the genes

Usage

compute.frequencies.scores(data, filter.threshold = 1, analysis.mode = "Log2")
compute.frequencies.scores(data, filter.threshold = 1, analysis.mode = "Log2")

Arguments

`data`	input data as result of the function perform.query
`filter.threshold`	threshold to filter for a minimum number of citations for the genes
`analysis.mode`	logaritmic scores to be computed, i.e., log10, log2, natural log or log5

Value

the computed scores

compute.oncoscore

Description

compute the OncoScore for a list of genes

Usage

compute.oncoscore(
  data,
  filter.threshold = 0,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL,
  filter.invalid = TRUE
)
compute.oncoscore(
  data,
  filter.threshold = 0,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL,
  filter.invalid = TRUE
)

Arguments

`data`	input data as result of the function perform.query
`filter.threshold`	threshold to filter for a minimum number of citations for the genes
`analysis.mode`	logaritmic scores to be computed, i.e., log10, log2, natural log or log5
`cutoff.threshold`	threshold to be used to asses the oncogenes
`file`	should I save the results to text files?
`filter.invalid`	auto-remove genes with invalid count

Value

the computed OncoScores and the clusters for the genes

Examples

data(query)
compute.oncoscore(query)

data(query)
compute.oncoscore(query)

compute.oncoscore.from.region

Description

Perform OncoScore analysis on a given chromosomic region

Usage

compute.oncoscore.from.region(
  chromosome,
  start = NA,
  end = NA,
  gene.num.limit = 100,
  filter.threshold = NA,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL
)
compute.oncoscore.from.region(
  chromosome,
  start = NA,
  end = NA,
  gene.num.limit = 100,
  filter.threshold = NA,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL
)

Arguments

`chromosome`	chromosome to be retireved
`start`	initial position to be used
`end`	final position to be used
`gene.num.limit`	A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed
`filter.threshold`	threshold to filter for a minimum number of citations for the genes
`analysis.mode`	logaritmic scores to be computed, i.e., log10, log2, natural log or log5
`cutoff.threshold`	threshold to be used to asses the oncogenes
`file`	should I save the results to text files?

Value

the computed scores

Examples

chromosome = 15
start = 200000
end = 300000

chromosome = 15
start = 200000
end = 300000

compute.oncoscore.timeseries

Description

perform the OncoScore time series analysis for a list of genes and data times

Usage

compute.oncoscore.timeseries(
  data,
  filter.threshold = 0,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL
)
compute.oncoscore.timeseries(
  data,
  filter.threshold = 0,
  analysis.mode = "Log2",
  cutoff.threshold = 21.09,
  file = NULL
)

Arguments

`data`	input data as result of the function perform.query.timeseries
`filter.threshold`	threshold to filter for a minimum number of citations for the genes
`analysis.mode`	logaritmic scores to be computed, i.e., log10, log2, natural log or log5
`cutoff.threshold`	threshold to be used to asses the oncogenes
`file`	should I save the results to text files?

Value

the performed OncoScores time series analysis

Examples

data(query.timepoints)
compute.oncoscore.timeseries(query.timepoints)

data(query.timepoints)
compute.oncoscore.timeseries(query.timepoints)

estimate.oncogenes

Description

estimate the oncoscore for the genes

Usage

estimate.oncogenes(data, cutoff.threshold = 21.09)
estimate.oncogenes(data, cutoff.threshold = 21.09)

Arguments

`data`	input data as result of the function compute.frequencies.scores
`cutoff.threshold`	threshold to be used to asses the oncogenes

Value

the computed scores and oncogenes

A list of genes

Description

This dataset contains a list of genes to be used in the analysis as an example

Usage

data(genes)
data(genes)

Format

rdata

Value

list of 5 elements

Source

example data

get.genes.from.biomart

Description

Get a gene list from biomart

Usage

get.genes.from.biomart(chromosome, start = NA, end = NA)
get.genes.from.biomart(chromosome, start = NA, end = NA)

Arguments

`chromosome`	chromosome to be retireved
`start`	initial position to be used
`end`	final position to be used

Value

A list of genes

Examples

chromosome = 15
start = 200000
end = 300000

chromosome = 15
start = 200000
end = 300000

get.list.from.xml

Description

process the result of the query

Usage

get.list.from.xml(webget)
get.list.from.xml(webget)

Arguments

webget

The result from the query to PubMed

Value

Processed result obtained from the query to PubMed

get.pubmed.driver.analysis

Description

query PubMed for a list of genes

Usage

get.pubmed.driver.analysis(keywords, gene)
get.pubmed.driver.analysis(keywords, gene)

Arguments

`keywords`	The set of keywords to be used for the query to PubMed
`gene`	The name of a gene to be used for the query to PubMed

Value

The frequency for the current gene retrieved with the query on the provided set of keywords

perform.query

Description

perforn the query to PubMed

Usage

perform.query(list.of.genes, gene.num.limit = 100, custom.search = NA)
perform.query(list.of.genes, gene.num.limit = 100, custom.search = NA)

Arguments

`list.of.genes`	The list of genes to be used in the queries to PubMed
`gene.num.limit`	A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed
`custom.search`	A custom set of keyworkds to be used when quering PubMed

Value

The frequencies of the genes in the cancer related documents and in all the documents retireved on PubMed

Examples

data(genes)

data(genes)

perform.query.from.region

Description

Perform the query to PubMed on a given chromosomic region

Usage

perform.query.from.region(
  chromosome,
  start = NA,
  end = NA,
  gene.num.limit = 100
)
perform.query.from.region(
  chromosome,
  start = NA,
  end = NA,
  gene.num.limit = 100
)

Arguments

`chromosome`	chromosome to be retireved
`start`	initial position to be used
`end`	final position to be used
`gene.num.limit`	A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed

Value

The frequencies of the genes in the cancer related documents and in all the documents retireved on PubMed

Examples

chromosome = 15
start = 200000
end = 300000

chromosome = 15
start = 200000
end = 300000

perform.query.timeseries

Description

perforn the query to PubMed for the time series analysis

Usage

perform.query.timeseries(
  list.of.genes,
  list.of.datatimes,
  gene.num.limit = 100,
  timepoints.limit = 10,
  custom.search = NA
)
perform.query.timeseries(
  list.of.genes,
  list.of.datatimes,
  gene.num.limit = 100,
  timepoints.limit = 10,
  custom.search = NA
)

Arguments

`list.of.genes`	The list of genes to be used in the queries to PubMed
`list.of.datatimes`	The list of time points to be used in the queries to PubMed
`gene.num.limit`	A limit to the genes to be considered in the analysis; this is done to limit the number of queries to PubMed
`timepoints.limit`	A limit to the time points to be considered in the analysis; this is done to limit the number of queries to PubMed
`custom.search`	A custom set of keyworkds to be used when quering PubMed

Value

The frequencies of the genes in the cancer related documents and in all the documents retireved on PubMed at the specified time points

Examples

data(genes)
data(timepoints)

data(genes)
data(timepoints)

plot.oncoscore

Description

plot the OncoScore for a list of genes

Usage

## S3 method for class 'oncoscore'
plot(
  x,
  gene.number = 5,
  main = "OncoScore",
  xlab = "score",
  ylab = "genes",
  file = NA,
  ...
)
## S3 method for class 'oncoscore'
plot(
  x,
  gene.number = 5,
  main = "OncoScore",
  xlab = "score",
  ylab = "genes",
  file = NA,
  ...
)

Arguments

`x`	input data as result of the function compute.OncoScore
`gene.number`	number of genes to print
`main`	the title
`xlab`	description of x asix (defaul score)
`ylab`	description of y asix (defaul genes)
`file`	where to save the plot
`...`	additional parameter to pass to the barplot function

Value

A plot

Examples

data(query)
result = compute.oncoscore(query)
plot.oncoscore(result)

data(query)
result = compute.oncoscore(query)
plot.oncoscore(result)

plot.oncoscore.timeseries

Description

plot the OncoScore for a list of genes

Usage

## S3 method for class 'oncoscore.timeseries'
plot(
  x,
  gene.number = 5,
  incremental = FALSE,
  relative = FALSE,
  main = "OncoScore",
  xlab = "timepoints",
  ylab = "score",
  legend.pos = "top",
  file = NA,
  ...
)
## S3 method for class 'oncoscore.timeseries'
plot(
  x,
  gene.number = 5,
  incremental = FALSE,
  relative = FALSE,
  main = "OncoScore",
  xlab = "timepoints",
  ylab = "score",
  legend.pos = "top",
  file = NA,
  ...
)

Arguments

`x`	input data as result of the function compute.OncoScore
`gene.number`	number of genes to print
`incremental`	display the OncoScore increment
`relative`	dispaly the incrementa as relative value
`main`	the title
`xlab`	description of x asix (defaul score)
`ylab`	description of y asix (defaul genes)
`legend.pos`	Position of the legend
`file`	where to save the plot
`...`	additional parameter to pass to the lines function

Value

A plot

Examples

data(query.timepoints)
result = compute.oncoscore.timeseries(query.timepoints)
plot.oncoscore.timeseries(result)

data(query.timepoints)
result = compute.oncoscore.timeseries(query.timepoints)
plot.oncoscore.timeseries(result)

The result of perform.web.query on genes

Description

This dataset contains the result of perform.web.query on genes

Usage

data(query)
data(query)

Format

rdata

Value

matrix 5 x 2

Source

example data

The result of perform.time.series.query on genes and timepoints

Description

This dataset contains the result of perform.time.series.query on genes and timepoints

Usage

data(query.timepoints)
data(query.timepoints)

Format

rdata

Value

list of 5 matrix 5 x 2

Source

example data

A list of timepoints

Description

This dataset contains a list of time points to be used in the analysis as an example

Usage

data(timepoints)
data(timepoints)

Format

rdata

Value

list of 5 elements

Source

example data

try.scan

Description

try to query the given URL

Usage

try.scan(getURL)
try.scan(getURL)

Arguments

getURL

The given URL

Value

Result obtained from PubMed