JMP Life Sciences Programming Guide | Macros Available for JMP Life Sciences Processes | Macro Descriptions

Macro Descriptions
AnnotationMacros
AnnotationMacros.sas contains macros used in graphical annotation routines.
ASEFMacros
ASEFMacros.sas is prepared for the Allele-specific Expression Filter process. It contains a collection of SAS macros that create DNA ratio vs. RNA ratio plots.
Bin2D
Bin2D.sas performs two-dimensional binning on spectral data.
BinaryResponseEffectSelectionMacros
BinaryResponseEffectSelectionMacros.sas includes macros used in cross-validation and learning-curve model comparison.
Class Vars
ClassVars.sas contains a macro for creating individual macro variables from variable lists, including indicator variables created from classification variables via PROC GLMMOD.
CopyNumberMacros
CopyNumberMacros.sas contains macros used for copy number analysis.
CrossValidationModelComparisonMacros
CrossValidationModelComparisonMacros.sas contains SAS macros used to manage and process the holdout iterations in the Cross Validation Model Comparison, Test Set Model Comparison, and Learning Curve Model Comparison processes used to evaluate the efficacy of different predictive models.
FastCCMacros
FastCCMacros.sas includes macros for rapid calculation of genetic case-control statistics.
GAMacros
GAMacros.sas contains macros pertaining to genetic algorithms for variable selection.
GenMacros
GenMacros.sas contains a set of macros used by the Genetics processes
IBDMacros
IBDMacros.sas contains macros used by the Genetics processes for identical-by-descent calculations.
InputEngineMacros
InputEngineMacros.sas defines the following macros for input engine processes:
%DesignParse
This macro imports the experimental design table (required for certain IEs) to extract the experimental information and the file name of each raw data file.
%DATParse
This macro imports the files with a data platform of Agilent (.txt), GenePix (.gpr), QuantArray (.txt), and Scanalyze (.dat) and combines them with the information from the experimental design table into a stacked SAS data set.
%CDFParse
This macro imports Affymetrix CDF file (text version) into a SAS data set, which is used to decode Affymetrix .cel and .chp files.
%CELParse
This macro imports Affymetrix .cel files (probe data stored in text or binary versions), which are based on the corresponding CDF file and combines them with the information from the experimental design table into a stacked SAS data set.
%CHPParse
This macro imports Affymetrix .chp files (signal summarized data), which are based on the corresponding CDF file and combines them with the information from the experimental design table into a stacked SAS data set.
%TableParse
This macro imports raw data files stored in text (tab delimited or comma separated), Excel, or SAS data set formats and combines them with the information from the experimental design table into a stacked SAS data set.
%Skip_Header_Import
This macro is used for Agilent (.txt) and GenePix (.gpr) IEs.
%Skip_Header_Import_2
This macro is used for the Import Individual Text, CSV, or Excel Files process, and the ScanAlyze IEs.
%CheckInputs
This macro checks certain required input parameters for the IEs that require an experiment design file.
%BeforeDataParse
This macro invokes DesignParse.
%AfterDataParse
This macro checks the final combined data set.
%Packaging
This macro wraps up package macros.
LoessModelMacros
LoessModelMacros.sas contains macros used in Loess Model Normalization for expression arrays.
MixedModelMacros
This file defines the primary computational macros used in ANOVA Normalization, Mixed Model Normalization, ANOVA, and Mixed Model Analysis.
MultipleTestingAdjustmentMacros
MultipleTestingAdjustmentMacros.sas includes macros used for adjusting p-values for multiple testing.
PartitionTreesMacros
PartitionTreesMacros.sas includes macros used to construct the traditional tree model using PROC GENESELECT. These macros support the TREE method in predictive modeling processes.
PCA_VCA
PCA_VCA.sas defines a macro for performing a variance components analysis on principal components. It is called from the Correlation and Principal Components process.
PLS_PCA
PLS_PCA.sas defines a macro invoking the PLS procedure (PROC PLS) to calculate principal components or partial least squares. This macro is used in the Principal Components and Partial Least Squares processes.
PredMacros
PredMacros.sas defines the principal macros used in the predictive modeling processes (Discriminant Analysis, K Nearest Neighbor, Distance Scoring, Logistic Regression, Partial Least Squares, Partition Trees, and Radial Basis Machine), including macros for k-fold cross-validation and genetic algorithm variable selection.
qtlUtilityMacros
qtlUtilityMacros.sas includes macros used for gentics QTL analysis.
Reorder
This macro is used by several processes that reorder the rows of an annotation data set to match the order of the columns of a wide data set.
RMAMacros
RMAMacros.sas includes macros for performing robust multichip anova normalization.
SeedMacros
SeedMacros.sas includes macros for handling random number seeds
SNPTraitAssocMacro
This macro is used by several to the association testing processes.
SurfacePlot
Surface Plot.sas defines a macro for drawing a color surface plot with contours underneath. This macro is used in the Surface Summary process.
TestSetModelComparisonMacros
TestSetModelComparisonMacros.sas includes macros for the Test Set Model Comparison under Predictive Modeling.
UtilityMacros
UtilityMacros.sas defines the following useful short macros utilized in most IEs and processes. You should %include UtilityMacros.sas at the beginning of any new process that you write, since it sets up several important macros and automatically runs the UtilInit macro.
%AddSuffixToDataName
This macro adds a suffix to a name.
%CheckAnno
This macro checks input parameters that correspond to annotation data.
%CheckBinary
This macro checks numeric variables to determine whether or not they are binary. Returns a value of 0 if all values are missing, 1 if there is a single value, 2 if there are two values, and 3 if there are three or more values.
%CheckBinaryChar
This macro checks numeric variable to determine whether or not they are binary. Returns a value of 0 if all values are missing, 1 if there is a single value, 2 if there are two values, and 3 if there are three or more values.
%CheckByVars
This macro screens out the precedent key word descending in a list of variables.
%CheckDataName
This macro checks whether a user-provided data name is a valid SAS data set name. If not, this macro modifies the data set name to a valid SAS data set name.
%CheckEndSlash
This macro checks a slash character for Windows or Linux operating systems.
%CheckExcel
This macro checks an Excel file and OS system.
%CheckForBlank
This macro checks whether the required input parameter is empty.
%CheckInData
This macro checks input data sets for compatibility with an experimental design data set.
%CheckJSL
This macro checks JSL names.
%CheckLabel
This macro checks whether the specified variable has an associated label.
%CheckLengthForMerging
This macro checks SAS variable lengths between two data sets to assure compatibility when merging.
%CheckListVarExist
This macro checks for the existence of a list of variables in a SAS data set.
%Checkrc
This macro checks the return code for a function.
%CheckVarExist
This macro checks for the existence of specified variables in a specified data set.
%ClockStart
This macro starts a timer.
%ClockStop
This macro stops a timer.
%ConvertFilePaths
This macro converts file paths between Windows and Linux.
%ConvertInputDataSet
This macro assigns a full path to a data set.
%ConvertInputFile
This macro assigns a full path to a file.
%CopySettingFile
This macro copies a setting file from an input folder to an output folder.
%ExitAndRetrieveLogLstFromJMP
This macro is run after a process to capture the SAS log and list file and perform final clean up.
%ExitSDSProcess
This macro performs ending tasks for a process.
%ExpandVars
This macro creates a list of variables separated by spaces. This macro is used for list-style specification of variables.
%FileFilter
This macro filters the files at a specified location and retains the filtered files in a data set.
%GetFileSize
This macro determines the size of a file.
%GetLevels
This macro extracts levels for a class variable.
%GetLineLoc
This macro extracts the physical starting location of the specified line in a text file.
%GetOrigFileName
This macro obtains and saves an original file name.
%GetVars
This macro extracts variables for a data set.
%GroupMacroVars
This macro is used to create various macro variables corresponding to a set of grouping variables.
%ImportScanRows
This macro modifies the number of scanning rows that are used for the IMPORT procedure (PROC IMPORT).
%LaunchExternalProgram
This macro launches an external program using Java.
%LaunchFile
This macro uses Java to launch each specified file.
%LaunchSASClean
This macro launches sasclean.jsl.
%MakeVarList
This macro creates a list of variables that contains a specified prefix from a given data set.
%MergeAnno
This macro merges annotation data into a SAS data set.
%Merge2sets
This macro merges two data sets using the specified merging keys.
%Naming
This macro checks the SAS variable naming convention for a given data set.
%NObsVars
This macro extracts the numbers of observations and variables for a given data set.
%PathName
This macro determines the path and file name from a full reference.
%PackageBegin
This macro starts a packaging process.
%PackageEnd
This macro finishes a packaging process.
%PackageInsertDataset
This macro inserts SAS data sets into a package.
%PackageInsertFile
This macro inserts files into a package.
%PackageInsertHtml
This macro inserts .html files into a package.
%PackagePublish
This macro binds and publishes packages.
%PrepHTML
This macro prepares .html output files.
%PrepOutFile
This macro prepares output text files.
%PrepOutDS
This macro prepares output data sets.
%PrintTimeFor
This macro prints the time.
%RemoveData
This macro removes a data set.
%RemoveFile
This macro removes/deletes a specified file.
%RemoveWord
This macro removes a word from a blank delimited string.
%RenameFIle
This macro uses Java to rename a file.
%Search_and_Replace
This macro searches a string for a word and replaces it with another.
%ShowTime
This macro writes the current day and time to the log with a prefixing message.
%Stack
This macro creates a stacked data set from the combination of a tall data set and an experimental design file.
%Stack_to_Tall
This macro creates a tall data set from a stacked data set.
%Sweep
This macro sweeps a symmetric matrix within a data step.
%TrimStringVariabe
This macro trims string variables to a specified length.
%UtilInit
This macro initializes several important macro variables and is run when %including UtilityMacros.sas.
%VarAttributes
This macro extracts the attributes (length and type) of the variables from an input file.
WebSearchJSL
Web Search JSL.sas defines macros for creating JSL code to assign labels and generates a Bioinformatics Web Search dialog box in JMP using the global variables AnnoInFile, AnnoLabel, AnnoData, AnnoAccession, and AnnoMergeVar. It is designed to be %included within analytical process SAS code that is generating JSL in the same fashion.
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