addColumns

Adds one or more specified columns to the table.

•    name: <text> (multiple) - the name(s) of the name column(s) to be affected.

•    annotation: <text> (multiple) 0 the name(s) of the annotation column(s) to be affected.

•    expInfoSet: <text> (multiple) - the name(s) of the expInfoSet column(s) to be affected.

•    expSignalSet: <text> (multiple) - the name(s) of the expSignalSet column(s) to be affected.

•    isPrimarySignal: true or false - the primary expSignalSet column to be affected.

•    scale: one of Linear, Log2, Log10, MaxValue - the DataPointScale of the primary signal column to be affected.

•    experiment: <text> (multiple) - the experiment name(s) for which to affect the specified column(s).

•    experimentRegex: <text> - an experiment regex to find the experiments for which to affect the specified column(s).

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

appInfo

Gets application information.

•    file: <text> - the path of a file to which to write the information (if not provided or empty, the message is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

closeView

Closes an open view.

•    viewNumber: <num> - the number of the open view of the same type, if more than one is open.

•    viewType: <text> - the name of the type of view to open.

createExperimentCategory

Creates a new experiment category.

•    name: <text> - the name of the new category to create.

•    userNotes: <text> - the user notes of the new category to create.

•    experiment: <text> (multiple) - the names of any experiments which should be placed in the category.

•    experimentRegex: <text> - a regex to find the names of any experiments which should be placed in the category.

•    experimentType: <text> - the type of experiments which should be placed in the category.

deleteSet

Deletes a saved set from the project.

set: <text> - the name of the set to delete.

dumpSNPs

Records in a human-readable format.

•    file: <text> - SNP file path.

•    dumpFile: <text> - dump (output) text file path.

•    startPosition: <num> - start position of the range from which SNPs should be dumped.

•    endPosition: <num> - end position of the range from which SNPs should be dumped.

•    appendToFile: true or false - if true, append to the file given; if false, overwrite it.

duplicateView

Duplicates an open view.

•    viewNumber: <num> - the number of the open view of the same type, if more than one is open.

•    viewType: <text> - the name of the type of view to open.

exportRows

Exports the specified data points. 

•    exportSpace: one of All, Selection, Set - the scope of the export to be executed, can specifiy All or Set.

•    setname: <text> - the name of the gene set to be used by the export.

•    file: <text> - the name of the file to be used as output by the export. 

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

exportStatsOutput

Exports the statistical output in a text report.

•    viewNumber: <num> - the number of the open view of the same type, if more than one is open.

•    file: <text> - the file name/path to which to export (will be overwritten).

•    format: <value> - the number of the open view of the same type, if more than one is open.

importAnnotations

Imports annotations into the project.

•    file: <text> - the path to the file to import.

•    useCustom: true or false.

•    forceCustom: true or false.

•    delimiter: one of Tab, Comma, Semicolon, Space.

•    commentChars: <text>.

•    skipLines: <num>.

•    noHeaderLine: true or false.

•    colNum: <num> (multiple).

•    colType: <value>.

loadProject

Loads a project file into ArrayStar. 

file: <text> - file path.

message

Shows a simple message to the user.

•    showDateTime: true or false - show the date and time.

•    caption: <text> - a caption to display with the message (ignored if writing to a file).

•    message: <text> - the text to display to the user or write to a file.

•    file: <text> - the path of a file to which to write the message (if not provided or empty, the message is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

openFilteringWindow

Open the advanced filtering window.

selected: true or false – specifies whether the filtering window should start as 'filter selected'.

openView 

Opens a new view.

viewType: <text> - the name of the type of view to open.

printProjectDataPointStats 

Prints statistical summary information about project data points.

•    caption: <text> - a caption to display with the message (ignored if writing to a file).

•    file: <text> - the path of a file to which to write the summary (if not provided or empty, the message is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

printProjectExpStats 

Prints summary information about project experiments.

•    caption: <text> - a caption to display with the message (ignored if writing to a file).

•    file: <text> - the path of a file to which to write the summary (if not provided or empty, the message is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

printSetInfo

Prints information about a saved set of data points.

•    set: <text> - the name of the set.

•    caption: <text> - a caption to display with the message (ignored if writing to a file).

•    file: <text> - the path of a file to which to write the summary (if not provided or empty, the message is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

printSnpPreprocessingPerformance

Logs information about the performance of SNP preprocessing.

•    file: <text> - the path of a file to which to write the performance information (if not provided or empty, this is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

quickFilterTable 

Displays the data points by the specified quick filter.

•    filter: one of None, All, Selected, CurrSet, Set, CustomSNPs, UserSNP, CodingSNP, NonsynonSNP, NonsenseSNP - the filter type used to specify the datapoints to be displayed.

•    setname: <text> - the name of the gene set to be used by the quick filter.

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

quit 

Quits running the script.

quitProgram

Quits the program running the script.

forceImmediateQuit: true or false - if true, attempts to force the program to quit without saving anything (the project, preferences, etc.).

readTimer 

Reads an elapsed time (i.e. wall clock) timer.

•    name: <text> - the name of the timer to use, or if left empty, the default timer.

•    message: <text> - a message to display or write with the timer.

•    file: <text> - the path of a file to which to write the timer information (if not provided or empty, this is displayed instead).

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

removeColumns

Removes one or more specified columns from the table.

•    name: <text> (multiple) - the name(s) of the name column(s) to be affected.

•    annotation: <text> (multiple) - the name(s) of the annotation column(s) to be affected.

•    expInfoSet: <text> (multiple) - the name(s) of the expInfoSet column(s) to be affected.

•    expSignalSet: <text> (multiple) - the name(s) of the expSignalSet column(s) to be affected.

•    isPrimarySignal: true or false – specifies whether the primary expSignalSet column should be affected.

•    scale: one of Linear, Log2, Log10, MaxValue - the DataPointScale of the primary signal column to be affected.

•    experiment: <text> (multiple) - the experiment name(s) for which to affect the specified column(s).

•    experimentRegex: <text> - an experiment regex to find the experiments for which to affect the specified column(s).

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

reportSetCrossIntersection

Creates a report table of set cross-intersections.

•    rowSets: <text> (multiple) - the sets which make up the rows (prepend with \\ or two backslashes to complement a set).

•    columnSets: <text> (multiple) - the sets which make up the columns (prepend with \\ or two backslashes to complement a set).

•    file: <text> - the path of a file to which to write the table.

•    overwriteFile: true or false - if a file is provided, specifies whether it should be overwritten (if false, the file is appended to).

runscript

Runs another script nested within this one, optionally repeated over a table of substitution variable values.

•    inline: <text> (multiple) - inline script command(s) to run first.

•    script: <text> - script file to run.

•    vars: <text> - comma-separated variable names to use with 'table' or 'values' substitution.

•    values: <text> (multiple) - comma-separated set(s) of inline values to substitute for the variables in 'vars' (analogous to normal line(s) in 'table').

•    table: <text> - tab-delimited table file over which to repeat the script commands (first line is a set of substitution variable names if 'vars' is not set, other lines are sets of variable values to iterate over).

saveProject

Saves a project file from ArrayStar.

file: <text> - file path.

selectRows

Selects the specified data points.

•    selectionSpace: one of All, Set - the scope of the selection to be executed, can specify All or Set.

•    setname: <text> - the name of the gene set to be used by the selection.

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

set $name

Sets a substitution variable to the given value. It can then be used as $name or ${name} in other script values.

value

setComplement

Creates a set which is the complement of another set.

•    name: <text> - the name of the new set to create.

•    set: <text> - the name of the set to complement.

setCurrentView

Sets which view is the current one.

•    viewNumber: <num> - the number of the open view of the same type, if more than one is open.

•    viewType: <text> - the name of the type of view to open.

setIntersect

Creates a set which is the intersection of two or more sets.

•    name: <text> - the name of the new set to create.

•    sets: <text> (multiple) - the names of the sets from which the intersection will be created (prepend with \\ or two backslashes to complement a set).

setSnpPreprocessingOptions

Sets preprocessing options for SNPs.

•    QuantificationMethod: one of Counts, Weights

•    MinPnotref: <num>

•    MinSNPPct: <num>

•    MinDepth: <num>

•    SNPRegionFilter: one of AllSNPs, GeneRegions, RNAs, NonCodingRNAs, CodingAndSplice, Intergenic, TargetedCaptureRegions

•    SNPTypeFilter: one of AnyChange, AnyNonSynonymousChange

•    MinNumExperimentsMatching: <num>

•    IgnoreMinNumExpsNonSynonymous: true or false

•    IgnoreMinNumExpsGeneDisrupting: true or false

•    ImportAnnoDB: true or false

•    AnnoDBUsername: <text>

•    AnnoDBPassword: <text>

•    AnnoDBDataSet: <text>

•    AnnoDBServerURL: <text>

•    ImportAnnoDBVariantsOnly: true or false

•    ImportAnnoDBNonSynonymousOnly: true or false

•    IncludeDBSNPData: true or false

•    IncludeUserSNPData: true or false

•    ForceIncludeAllSNPData: true or false

•    ForceIncludeAllUserSNPData: true or false

•    LimitToUserSNPData: true or false

setUnion

Creates a set which is the union of two or more sets.

•    name: <text> - the name of the new set to create.

•    sets: <text> (multiple) - the names of the sets from which the union will be created (prepend with \\ or two backslashes to complement a set).

sortTable

Sorts the table by the specified column.

•    descending true or false - specifies whether the sort order for the specified column is descending.

•    name: <text> (multiple) - the name(s) of the name column(s) to be affected.

•    annotation: <text> (multiple) - the name(s) of the annotation column(s) to be affected.

•    expInfoSet: <text> (multiple) - the name(s) of the expInfoSet column(s) to be affected.

•    expSignalSet: <text> (multiple) - the name(s) of the expSignalSet column(s) to be affected.

•    isPrimarySignal: true or false – specifies whether the primary expSignalSet column is affected.

•    scale: one of Linear, Log2, Log10, MaxValue - the DataPointScale of the primary signal column to be affected.

•    experiment: <text> (multiple) - the experiment name(s) for which to affect the specified column(s).

•    experimentRegex: <text> - an experiment regex to find the experiments for which to affect the specified column(s).

•    table: one of Gene, IPFragment, IPPeak, SNP, ExperimentAttribute, Exon, Isoform, MaxValue - the data type of the gene table for which columns will be affected.

startProject 

Starts a new project.

•    workflow: one of Empty, Microarray, RNASeq, SNP, ChIPSeq, CNV, miRNA – the workflow to start in the new project.

•    loadFile: <text> (multiple) - import one or more files into the new project.

•    addToCurrent: true or false – specifies whether the new data (if any) should be added to the current project.

startTimer

Starts an elapsed time (i.e. wall clock) timer.

name: <text> - the name of the timer to use, or if left empty, the default timer.

statsCrossR2

Runs Cross-R.