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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