Package 'PerseusR'

Title: Perseus R Interop
Description: Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.
Authors: Jan Rudolph <[email protected]>
Maintainer: Jan Rudolph <[email protected]>
License: MIT + file LICENSE
Version: 0.3.4
Built: 2025-03-12 05:30:30 UTC
Source: https://github.com/cox-labs/perseusr

Help Index

Get annotation columns

Description

Get annotation columns

Usage

annotCols(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
annotCols(mdata)

Set annotation columns

Description

Set annotation columns

Usage

annotCols(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
value <- data.frame(d=c('d', 'e', 'f'))
annotCols(mdata) <- value

Get annotation rows

Description

Get annotation rows

Usage

annotRows(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
annotRows(mdata)

Set annotation rows

Description

Set annotation rows

Usage

annotRows(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
value <- data.frame(y=factor(c('2','2')))
annotRows(mdata) <- value

Coerces a MatrixData into an ExpressionSet

Description

Coerces a MatrixData object into an ExpressionSet object

Usage

as.ExpressionSet.matrixData(mdata)

Arguments

mdata

a matrixData object

Details

function to convert a matrixData ExpressionSet

Value

returns an ExpressionSet object

Examples

mD <- matrixData(
main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(b=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))

eSet <- as(mD, "ExpressionSet")
print(eSet)

Coerces an ExpressionSet into a MatrixData

Description

function to convert an ExpressionSet object into a matrixData

Usage

as.matrixData.ExpressionSet(ExpressionSet)

Arguments

ExpressionSet

an ExpressionSet object

Value

returns a matrixData object

Examples

eSet <- eSet <- Biobase::ExpressionSet(matrix(1:10, ncol = 2))
mD <- as(eSet, "matrixData")
print(mD)

Bool parameter value

Description

Extract the value chosen in an BoolParam

Usage

boolParamValue(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The selected boolean

Examples

tmp <- tempfile(fileext = ".xml")
write('<BoolParam Name="test_bool">\n<Value>false</Value>\n</BoolParam>', file=tmp)
parameters <- parseParameters(tmp)
boolParamValue(parameters, "test_bool")

Create annotation rows

Description

Create the annotation rows data.frame from the list of comment rows parsed from the input file and the main columns indicator

Usage

create_annotRows(commentRows, isMain)

Arguments

commentRows

list of comment rows
isMain

logical array indicating all main columns

See Also

used by read.perseus

Get column description

Description

Get column description

Usage

description(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
description=c('aaa', 'bbb', 'ccc'))
description(mdata)

Set column description

Description

Set column description

Usage

description(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
value <- c('aaa', 'bbb', 'ccc')
description(mdata) <- value

Get imputation of main data frame

Description

Get imputation of main data frame

Usage

imputeData(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
imputeData=data.frame(impute=c('False', 'True', 'False')))
imputeData(mdata)

Set imputation of main data frame

Description

Set imputation of main data frame

Usage

imputeData(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
imputeData=data.frame(impute=c('False', 'True', 'False')))
value <- data.frame(impute=c('True', 'True', 'True'))
imputeData(mdata) <- value

Infer Perseus type annotation row from DataFrame column classes

Description

Infer Perseus type annotation row from DataFrame column classes

Usage

infer_perseus_annotation_types(df, typeMap)

Arguments

df

The data.frame
typeMap

A list with elements 'Perseus' and 'R'. The ordering determines the mapping

Value

A vector with perseus type annotations

See Also

Based on mapvalues

matrixData initializer

Description

Initializes the annotCols data frame to have the same number of rows as the main data. This might not be the cleanest solution.

Usage

## S4 method for signature 'matrixData'
initialize(.Object, ...)

Arguments

.Object

Initialized object
...

Additional arguments

Int parameter value

Description

Extract the value chosen in an IntParam

Usage

intParamValue(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The selected number

Examples

tmp <- tempfile(fileext = ".xml")
write('<IntParam Name="test_int">\n<Value>2</Value>\n</IntParam>', file=tmp)
parameters <- parseParameters(tmp)
intParamValue(parameters, "test_int")

Get main columns

Description

Gets the main columns (main matrix) of a matrixData object as a data.frame object

Usage

main(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
main(mdata)

Set main columns

Description

Set main columns

Usage

main(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))))
value<-data.frame(c=c(0,0,0), d=c(1,1,1))
main(mdata) <- value

matrixData constructor

Description

matrixData constructor

Usage

matrixData(...)

Arguments

...

main, annotCols, annotRows, description, imputeData, qualityData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, names,matrixData-method, qualityData<-, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
description=c('aaa', 'bbb', 'ccc'),
imputeData=data.frame(impute=c('False', 'True', 'False')),
qualityData=data.frame(quality=c('0', '1', '0')))

MatrixData

Description

MatrixData

Slots

main

Main expression data.frame.

annotCols

Annotation Columns data.frame.

annotRows

Annotation Rows data.frame.

description

Column descriptions.

imputeData

Imputation data.frame.

qualityData

Quality values data.frame.

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData, names,matrixData-method, qualityData<-, qualityData

MatrixDataCheck: a function to check the validity of an object as a perseus data frame

Description

Check perseus compatibility of an object

Usage

MatrixDataCheck(object, ...)

## Default S3 method:
MatrixDataCheck(object = NULL, main, annotationRows,
  annotationCols, descriptions, imputeData, qualityData, all_colnames, ...)

## S3 method for class 'matrixData'
MatrixDataCheck(object, ...)

## S3 method for class 'list'
MatrixDataCheck(object, ...)

## S3 method for class 'ExpressionSet'
MatrixDataCheck(object, ...)

Arguments

object

object to check consistency with perseus data frames
...

additional arguments passed to the respective method
main

Main Data frame
annotationRows

Rows containing annotation information
annotationCols

Columns containing annotation information
descriptions

Descriptions of all the columns
imputeData

Is imputed or not
qualityData

quality number
all_colnames

The colnames to be used

Value

a logical indicating the validity of the object (or series of objects) as a perseus DF or the string of errors

NULL

NULL

NULL

Examples

require(PerseusR)

mat <- matrixData(
    main=data.frame(a=1:3, b=6:8),
    annotCols=data.frame(c=c('a','b','c')),
    annotRows=data.frame(x=factor(c('1','1'))))

MatrixDataCheck(mat)

Multiple choice value

Description

Extract the value selected in a MultiChoiceParam.

Usage

multiChoiceParamValue(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The string representing the value

Examples

write('<MultiChoiceParam Name="test_multi">\n<Value>\n<Item>1</Item>\n<Item>2</Item>\n</Value>\n
<Values>\n<Item>A</Item>\n<Item>B</Item>\n</Values>\n</MultiChoiceParam>', file='tmp.xml')
parameters <- parseParameters("tmp.xml")
multiChoiceParamValue(parameters, "test_multi")

Get names

Description

Get the column names of main and annotation columns.

Usage

## S4 method for signature 'matrixData'
names(x)

Arguments

x

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, qualityData<-, qualityData

Column names of main and annotation columns

Description

Column names of main and annotation columns

Usage

## S3 method for class 'matrixData'
names(x)

Arguments

x

matrixData

Parse parameters

Description

Parse parameters from the parameters xml file.

Usage

parseParameters(paramFile)

Arguments

paramFile

Parameters xml file

Examples

tmp <- tempfile(fileext = ".xml")
write('<IntParam Name="test_int">\n<Value>2</Value>\n</IntParam>', file=tmp)
parameters <- parseParameters(tmp)

Get quality values of main data frame

Description

Get quality values of main data frame

Usage

qualityData(mdata)

Arguments

mdata

matrixData

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData<-

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
qualityData=data.frame(quality=c('1', '1', '1')))
qualityData(mdata)

Set quality values of main data frame

Description

Set quality values of main data frame

Usage

qualityData(mdata) <- value

Arguments

mdata

matrixData
value

value

See Also

Other matrixData basic functions: annotCols<-, annotCols, annotRows<-, annotRows, description<-, description, imputeData<-, imputeData, main<-, main, matrixData-class, matrixData, names,matrixData-method, qualityData

Examples

mdata <- matrixData(main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(c=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
qualityData=data.frame(quality=c('1', '1', '1')))
value <- data.frame(quality=c('0', '0', '0'))
qualityData(mdata) <- value

Read Perseus matrix files

Description

Read the custom Perseus matrix file format *.txt into R.

Usage

read.perseus.default(con, check = TRUE, additionalMatrices = FALSE)

read.perseus.as.list(con, check = TRUE)

read.perseus.as.matrixData(con, check = TRUE,
  additionalMatrices = FALSE)

read.perseus.as.ExpressionSet(con, check = TRUE)

read.perseus(con, check = TRUE, additionalMatrices = FALSE)

Arguments

con

A connection object or the path to input file
check

Logical indicating whether to check for the validity of the exported object (slightly slower)
additionalMatrices

Logical indication whether to write out quality and imputation matrices in perseus format

Value

Defaults to a matrixData object.

Functions

  • read.perseus.default: Returns a list used internally to generate all other outputs

  • read.perseus.as.list: Returns explicitly as a list

  • read.perseus.as.matrixData: Returns explicitly as a specialized matrix data object

  • read.perseus.as.ExpressionSet: Returns a bioconductor expression set object

Note

Limitations to column names in R still apply. Column names valid in Perseus, such as 'Column 1' will be changed to 'Column.1'

If the provided connection con is a character string, it will assumed to be a file path. A connection which is not seekable (see isSeekable) will be written to a temporary file. Any connection will be closed when read.perseus exits. read.perseus.as.list, read.perseus.as.matrixData and read.perseus.as.ExpressionSet are also available depending on the class desired as an output

See Also

write.perseus

matrixData

Examples

tmp <- tempfile(fileext = ".txt")
write('Column_1\tColumn_2\tColumn_3
#!{Description}\t\t
#!{Type}E\tE\tE
-1.860574\t-0.3910594\t0.2870352
NaN\t-0.4742951\t0.849998', file=tmp)
mdata <- read.perseus(tmp)

Single choice index

Description

Extract the index chosen in an BoolParam

Usage

singleChoiceParamInd(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The selected index

Examples

tmp <- tempfile(fileext = ".xml")
write('<SingleChoiceParam Name="test_single">\n<Value>1</Value>\n
<Values>\n<Item>A</Item>\n<Item>B</Item>\n</Values>\n</SingleChoiceParam>', file=tmp)
parameters <- parseParameters(tmp)
singleChoiceParamInd(parameters, "test_single")

Single choice value

Description

Extract the value selected in a SingleChoiceParam.

Usage

singleChoiceParamValue(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The string representing the value

Examples

tmp <- tempfile(fileext = ".xml")
write('<SingleChoiceParam Name="test_single">\n<Value>1</Value>\n
<Values>\n<Item>A</Item>\n<Item>B</Item>\n</Values>\n</SingleChoiceParam>', file=tmp)
parameters <- parseParameters(tmp)
singleChoiceParamValue(parameters, "test_single")

String parameter value

Description

Extract the value chosen in an StringParam

Usage

stringParamValue(parameters, name)

Arguments

parameters

The parameters object (see parseParameters)
name

The name of the parameter

Value

The selected string

Examples

write('<StringParam Name="test_string">\n<Value>"test"</Value>\n</StringParam>', file='tmp.xml')
parameters <- parseParameters("tmp.xml")
stringParamValue(parameters, "test_string")

write.perseus: function to generate a perseus-readable text document

Description

Write data to a perseus text file or connection

Write Data to file in the custom Perseus matrix file format.

Usage

write.perseus(object = NULL, con = NULL, ...)

## Default S3 method:
write.perseus(object = NULL, con = NULL, main,
  annotCols = NULL, annotRows = NULL, descr = NULL,
  imputeData = NULL, qualityData = NULL, ...)

## S3 method for class 'matrixData'
write.perseus(object, con, ...)

## S3 method for class 'list'
write.perseus(object, con, ...)

## S3 method for class 'data.frame'
write.perseus(object, con, annotCols = NULL, ...)

## S3 method for class 'matrix'
write.perseus(object, con, annotCols = NULL, ...)

## S3 method for class 'ExpressionSet'
write.perseus(object, con, ...)

Arguments

object

an expressionSet, matrixData, list or table-like object.
con

A connection object or the path to output file
...

additional arguments passed to other functions
main

a data frame containing
annotCols

a df containing columns containing metadata (about the rows)
annotRows

a df containing columns containing metadata (about the columns)
descr

a character vector that describes the columns in main and in annotCols (in that order)
imputeData

a df containing imputations – True or False of main data frame
qualityData

a df containing quality values of main data frame

Value

writes to disk a perseus-interpretable text representation of an R object

NULL

NULL

NULL

NULL

NULL

See Also

read.perseus matrixData

Examples

df <- matrixData(
main=data.frame(a=1:3, b=6:8),
annotCols=data.frame(b=c('a','b','c')),
annotRows=data.frame(x=factor(c('1','1'))),
description=c('a','a','b'))
con <- textConnection('df1', 'w')
write.perseus(df, con)
close(con)