JMP Life Sciences Processes Call SAS PROCS

JMP Life Sciences 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 Life Sciences 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