JMP Genomics Processes Call SAS PROCS

JMP Genomics makes extensive use of SAS routines (called PROCs) in order to carry out all of its different functions and analyses. The table below lists the PROCs called by each process. It does not include the following PROCs, which are called extensively by every process: APPEND, CONTENTS, DATASETS, EXPORT, MEANS, PRINT, REGISTRY, SORT, SQL, and TRANSPOSE. Processes are listed alphabetically.

JMP Genomics Processes Call SAS PROCs

Process

SAS PROCs Called

ABI Analyst Input Engine

IMPORT, STDIZE

AE Narrative

FREQ, REPORT

AE Time to Event

LIFETEST

Affected Sib-Pair Tests

ALLELE, FORMAT, PSMOOTH

Affymetrix Annotation CSV Files

IMPORT

Affymetrix CNAT Input Engine

IMPORT, STDIZE

Affymetrix CN CHP Input Engine

IMPORT, STDIZE

Affymetrix Cytogenetics CEL Input Engine

FORMAT, G3D, IMPORT, KDE, LOESS, REG, STDIZE, SURVEYSELECT, UNIVARIATE

Affymetrix Cytogenetics CEL Input Engine

IMPORT, STDIZE

Affymetrix Exon and Whole Transcript Expression CEL Input Engine

FORMAT, G3D, IMPORT, KDE, STDIZE, UNIVARIATE

Affymetrix Expression CEL Input Engine

FORMAT, G3D, IMPORT, KDE, STDIZE, UNIVARIATE

Affymetrix Expression CHP Input Engine

This process calls no additional SAS PROCs

Affymetrix miRNA CEL Input Engine

FORMAT, G3D, IMPORT, KDE, LOESS, REG, STDIZE, SURVEYSELECT, UNIVARIATE

Affymetrix SNP CEL Input Engine

FORMAT, G3D, IMPORT, KDE, STDIZE, UNIVARIATE

Affymetrix SNP CHP Input Engine

IMPORT, STDIZE

Affymetrix Tiling Bar Input Engine

IMPORT

Affymetrix Tiling CEL Input Engine

IMPORT

Agilent Input Engine

IMPORT, STDIZE

Allele Specific Expression Filter

MULTTEST, REG

ANOVA

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

ANOVA Normalization

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Append

This process calls no additional SAS PROCs

ArrayTrack Input Engine

IMPORT, STDIZE

BAM Input Engine

IMPORT

Basic Expression Workflow

COPY

Basic RNA-Seq Workflow

COPY

Basic Tiling Workflow

COPY

Batch Normalization

FASTCLUS, GCHART, GPLOT, MIXED, PRINCOMP

Batch Scoring

UNIVARIATE

Bin (Copy Number)

This process calls no additional SAS PROCs

Bin Intensities or Read Counts

This process calls no additional SAS PROCs

BioConductor Expresso for Affymetrix

IMPORT, STDIZE

Bivariate One-Way ANOVA

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Build Genotype Probability Data Set

IML, REG, SUMMARY

Calculate Square Root of Matrix

IML

Case-Control Association

ALLELE, CASECONTROL, FORMAT, FREQ, MULTTEST, PSMOOTH

Change Labels

RANK

Check Required Variables

REPORT

Chromosome Color Theme

This process calls no additional SAS PROCs

Column Enrichment

FREQ, GLMMOD, MULTTEST, RANK, TPSPLINE

Combine Columns

This process calls no additional SAS PROCs

Combine Experiments

This process calls no additional SAS PROCs

Comment Report

REPORT

Compare Data Sets

COMPARE, IMPORT

Complete Genomics Input Engine

IMPORT

Control Set Normalization

This process calls no additional SAS PROCs

Copy Number/LOH COntrol Set Adjustment

This process calls no additional SAS PROCs

Correlation and Grouped Scatterplots

CORR, SURVEYSELECT

Correlation and Principal Components

CORR, FACTOR, GCHART, GPLOT, MIXED, PRINCOMP

Create Annotation Analysis Group Variable

This process calls no additional SAS PROCs

Cross Correlation

CORR

Cross Validation Model Comparison

FREQ, GENESELECT, HARRELL, LIFETEST, LOGISTIC

Data Filter

CORR, MIXED, MULTTEST

Data Standardize

STDIZE, UNIVARIATE

Difference Chooser

MIXED

Discriminant Analysis

CATALOG, CORR, DISCRIM, FASTCLUS, FREQ, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

Disproportionality Analysis

FREQ, IML, RANK

Distribution Analysis

KDE, SUMMARY

Distance Matrix

CLUSTER, DISTANCE, TREE

Distance Scoring

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

Eland Input Engine

IMPORT

Estimate Builder

MIXED

Expand Multiallelic Genotypes

ALLELE, FORMAT

Experimental Design File Builder

OPTIONS

Export SAS Transport File

COPY, CPORT

Export to GSEA Format

FREQ

Exposure Summary

FORMAT, LIFETEST, REPORT, SUMMARY

Expression QC Workflow

UNIVARIATE

Factor Analysis Normalization

FACTOR

Feature Flagger

FREQ, REPORT

Filter Intensities

UNIVARIATE

Findings ANOVA

FREQ, MIXED

Findings Distribution

FREQ

Gene Model Summary

IMPORT, UNIVARIATE

Gene Set Enrichment

FREQ, GLMMOD, MULTTEST, RANK

GenePix Input Engine

IMPORT, STDIZE

General Linear Model Selection

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GLIMMIX, GLMMOD, GLMSELECT, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

GxE Interaction

FREQ, GLM, IML, MIXED, REG

Haplotype Estimation

ALLELE, FORMAT, HAPLOTYPE, PSMOOTH

Haplotype Trend Regression

GLM, GLIMMIX, HAPLOTYPE, LOGISTIC, MULTTEST, PHREG, REG

HapMap Input Engine

IMPORT

Haseman-Elston Regression

ALLELE, FORMAT, MIXED, PSMOOTH

htSNP Selection

ALLELE, FORMAT, HTSNP, PSMOOTH

Hy’s Law Screening

FREQ

Illumina CN Input Engine

IMPORT, STDIZE

Illumina Expression Input Engine

IMPORT, STDIZE

Illumina miRNA Input Engine

IMPORT, KDE, LOESS, REG, STDIZE, SURVEYSELECT, UNIVARIATE

Illumina SNP Input Engine

IMPORT, STDIZE

QTL IM and CIM Analysis

IML, REG, REPORT, SUMMARY

Import a Designed Experiment from Text, CSV or Excel Files

IMPORT, STDIZE

Import Individual Text, CSV or Excel Files

IMPORT, STDIZE

Import SAS Transport Files

CIMPORT, COPY

Imputed SNP (Tall Format) Input Engine

IMPORT

Imputed SNP-Trait Association

ALLELE, FORMAT, GLIMMIX, LOGISTIC, MIXED, PHREG, PSMOOTH, SURVEYFREQ

Imputed SNP (Wide Format) Input Engine

IMPORT

Ingenuity Get Gene Pathways

IMPORT

K Matrix Compression

CLUSTER, IML, MIXED, TREE

K-Means Clustering

FASTCLUS

K Nearest Neighbors

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

KDMM Normalization

KDE, SUMMARY

Kinship Matrix

IML, INBREED

LD Block Creation

ALLELE, IML

LD tagSNP Selection

ALLELE, FORMAT, IML, PSMOOTH

Life Regression

LIFEREG

Linkage Disequilibrium

ALLELE, FORMAT, PSMOOTH

Linkage Map Order

IML, MDS, OPTMODEL

List Enrichment

FREQ, IMPORT

Loess Normalization

LOESS

Logistic Regression

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GENESELECT, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

Malecot LD Map

ALLELE, FORMAT, NLMIXED, PSMOOTH

MANOVA

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Marker Properties

ALLELE, FORMAT, PSMOOTH

Marker-Trait Association

ALLELE, FORMAT, GLIMMIX, LOGISTIC, MIXED, PHREG, PSMOOTH

Merge

This process calls no additional SAS PROCs

Merge CVMC Results

IMPORT

Merge Gene Sets

IMPORT

Missing Genotypes by Trait Summary

ALLELE, CASECONTROL, FORMAT, PSMOOTH

Mixed Model Analysis

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Mixed Model Normalization

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Mixed Model Power

MIXED

Multidimensional Scaling

MDS

Multiple SNP-Trait Association

GLIMMIX, GLM, LOGISTIC, MIXED, PHREG, PRINCOMP, PSMOOTH

One-Way ANOVA

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

Parse a Column

This process is a .jsl script and calls no SAS PROCs

Partial Least Squares

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, PLS, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

Partial Least Squares Normalization

GLMMOD, PLS

Partition (Copy Number )

FREQ, GENESELECT

Partition Trees

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GENESELECT, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

PCA for Population Stratification

ALLELE, CORR, FORMAT, GLMMOD, IML, MULTTEST, PLS, PRINCOMP, PSMOOTH, STDIZE, SUMMARY

Pedigree Input Engine

IMPORT

Phenotype Summary

FREQ

Pleiotrophic Association

ALLELE, GLM, PSMOOTH

PLINK Input Engine

IMPORT, STDIZE

P-Value Adjustment

MIXED, MULTTEST, STDIZE, TPSPLINE, UNIVARIATE

P-Value Browser

FORMAT, MULTTEST, PSMOOTH, TPSPLINE

P-Value Combination

PSMOOTH

Pedigree Input Engine

IMPORT, STDIZE

Phenotype Summary

FREQ

Population Genetic Distance

ALLELE, FORMAT, PSMOOTH

Population Measures

ALLELE, CLUSTER, FORMAT, PSMOOTH, TREE

Principal Components Analysis

GLMMOD, PLS, PRINCOMP, STDIZE, SUMMARY

Principal Component Scoring

IML, PLS

Pseudo Image

STDIZE, UNIVARIATE

Q-K Mixed Model

ALLELE, FORMAT, GLIMMIX, LOGISTIC, MIXED, PSMOOTH,SURVEYFREQ

QuantArray Input Engine

IMPORT, STDIZE

Quantitative TDT

ALLELE, FAMILY, FORMAT, GLM, IML, INBREED, MIXED, PSMOOTH, UNIVARIATE

Radial Basis Machine

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

Rank Rows

RANK

Rare Variant Association

IML, PLAN

Ratio Analysis

LOESS

Recode Genotypes

ALLELE, FORMAT, PSMOOTH

Recode Missing Genotypes

This process calls no additional SAS PROCs

Recombination and Linkage Groups

CLUSTER, IML, TREE

Relationship Matrix

CORR, DISTANCE, IML, PRINCOMP

Reorder

This process calls no additional SAS PROCs

RPM Scaling

STDIZE

Quantitative TDT

ALLELE, FAMILY, GLM, MIXED, UNIVARIATE

SAM Input Engine

IMPORT

SNP Interaction Discovery

CATALOG, CORR, DISCRIM, DISTANCE, FASTCLUS, FREQ, GENESELECT, GLIMMIX, GLMMOD, IML, LOGISTIC, MIXED, MULTEST, NPAR1WAY, RANK, REG, ROBUSTREG, STDIZE, STEPDISC, TPSPLINE, TTEST, UNIVARIATE

SNP Power

IML

SNP-SNP Interactions

FORMAT, GLIMMIX, LOGISTIC, MIXED, MULTTEST, PHREG, PSMOOTH

SNP-Trait Association

ALLELE, FORMAT, GLIMMIX, LOGISTIC, MIXED, PHREG, PSMOOTH

ScanAlyze Input Engine

IMPORT, STDIZE

Single Marker Analysis

IML, REG, REPORT, SUMMARY

Spectral 2D Peak Find

IML

Spectral 3D Align

KDE

Spectral 3D Plot

SPECTRAVIEW

Split Experiments

This process calls no additional SAS PROCs

Statistics for Columns

SUMMARY

Study Visit Report

FREQ, REPORT

Subset and Reorder Genetic Data

ALLELE, FORMAT, PSMOOTH

Surface Summary

FORMAT, G3D, KDE, UNIVARIATE

Survey SNP-Trait Association

ALLELE, FORMAT, PSMOOTH, SURVEYFREQ, SURVEYLOGIC, SURVEYREG

Survival Analysis

MULTTEST, PHREG, STDIZE, TPSPLINE

Survival Predictive Modeling

PHREG, MULTTEST

Survival Residuals

PHREG

TDT

ALLELE, FAMILY, FORMAT, PSMOOTH

TMM Normalization

KDE, UNIVARIATE

Track BAR Chart

This process calls no additional SAS PROCs

Track Gene GFF

This process calls no additional SAS PROCs

Track Gene Text

This process calls no additional SAS PROCs

Track Gene Web

This process is a .jsl script and calls no SAS PROCs

Track SNP Web

This process is a .jsl script and calls no SAS PROCs

Transform

This process calls no additional SAS PROCs

Treatment Emergent AE Summary

FORMAT, FREQ, REPORT, SUMMARY

Two-Way Plotter

GCHART, GPLOT, GREPLAY

Upper Quartile Scaling

UNIVARIATE

Variance Components

ALLELE, FORMAT, IML, INBREED, MIXED, PSMOOTH, UNIVARIATE

VCF Input Engine

IMPORT

Verify Gender of Samples

This process calls no additional SAS PROCs