PBAT
Description
PBAT: Tools for the statistical analysis of family-based association studies (FBAT).Developed by Christoph Lange, PBAT is intended to be used interactively on Helix. The program was not designed for batch use, but if you need to run large numbers of PBAT jobs, it is possible to run a swarm of PBAT jobs on the Biowulf cluster.
Version
Type pbat on command line
Sample session
The log file and output file will be under the current directory.% pbat ******************************************************* * * * * * * * * * * ********* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Christoph Lange 1/1/2006 v3.2 * * Department of Biostatistics * * Harvard School of Public Health * * * ******************************************************* Any key to clear screen Package for family-based association test ==================================================== (1) Power calculations for binary traits & multiple family-types (2) Power calculations for continuous traits & multiple family-types (3) Power & sample size calculations for case/control studies (4) Power & sample size calculations for quantitative traits in population-based studies (5) Data analysis tools for continuous traits (SNPs) (6) Data analysis tools for continuous traits (Haplotypes) (-1) Exit 0 ? 1 Log-file name: pbatlog1161718544 ? test1.log Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 1 Family design: =============== (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 1 Family design: =============== Change family-type: =================== Number of offspring per family: 0 ? 1 Number of missing parents(0,1,2): 0 ? Number of families: 0 ? 213 Ascertainment condition for proband 1: unaffected=0, affected=1, NA=2 0 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 Change family-type: =================== Number of offspring per family: 1 ? 2 Number of missing parents(0,1,2): 0 ? 1 Number of families: 213 ? 175 Additional offspring phenotyped? 1=yes 0=no 1 ? 0 Ascertainment condition for proband 1: unaffected=0, affected=1, NA=2 1 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 Change family-type: =================== Number of offspring per family: 2 ? 3 Number of missing parents(0,1,2): 1 ? Number of families: 175 ? Additional offspring phenotyped? 1=yes 0=no 0 ? Ascertainment condition for proband 1: unaffected=0, affected=1, NA=2 1 ? Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 Change family-type: =================== Number of offspring per family: 3 ? 2 Number of missing parents(0,1,2): 1 ? 2 Number of families: 175 ? 220 Additional offspring phenotyped? 1=yes 0=no 0 ? Ascertainment condition for proband 1: unaffected=0, affected=1, NA=2 1 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 Change family-type: =================== Number of offspring per family: 2 ? 3 Number of missing parents(0,1,2): 2 ? Number of families: 220 ? Additional offspring phenotyped? 1=yes 0=no 0 ? Ascertainment condition for proband 1: unaffected=0, affected=1, NA=2 1 ? Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? 3 Save design: =============== Enter file name: test1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 (1) Change family design (2) Load family design (3) Save family design or Press any other key to clear screen 0 ? Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 2 Genetic model: ================= Model: Add=0 Multi=1 Recessive=2 Dom=3: 0 Allele frequency of the disease allele: 0.2 Population prevalence of the disease: 0.3 Genetic attributable fraction of the allele: 0.1 Penetrance for AA: 0.8 Penetrance for AB: 0.5 Penetrance for BB: 0.3 Relative Risk RR1: 1.667 Relative Risk RR2: 2.667 Odds ratio OR1: 2.333 Odds ratio OR2: 9.333 Allelic odds ratio: 2.471 Allele frequency of the marker gene: 0.2 P(Disease allele A| Marker allele A): 1 D' : 1 (0) Return to main menu (1) Specify genetic model based on MOI, p, K & AF (2) Specify genetic model based on penetrance values & allele frequency (3) Specify genetic model based on MOI, p, K & odds-ratio (4) Specify genetic model based on MOI, p, K & allelic odds-ratio 0 ? Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 2 Genetic model: ================= Model: Add=0 Multi=1 Recessive=2 Dom=3: 0 Allele frequency of the disease allele: 0.2 Population prevalence of the disease: 0.3 Genetic attributable fraction of the allele: 0.1 Penetrance for AA: 0.8 Penetrance for AB: 0.5 Penetrance for BB: 0.3 Relative Risk RR1: 1.667 Relative Risk RR2: 2.667 Odds ratio OR1: 2.333 Odds ratio OR2: 9.333 Allelic odds ratio: 2.471 Allele frequency of the marker gene: 0.2 P(Disease allele A| Marker allele A): 1 D' : 1 (0) Return to main menu (1) Specify genetic model based on MOI, p, K & AF (2) Specify genetic model based on penetrance values & allele frequency (3) Specify genetic model based on MOI, p, K & odds-ratio (4) Specify genetic model based on MOI, p, K & allelic odds-ratio 0 ? 1 Specify genetic model based on MOI, p, K & AF Genetic model: ============== Model: Add=0 Multi=1 Recessive=2 Dom=3: 0 ? 2 Allele frequency of the disease gene: 0.2 ? .1 Increment in allele freq per iteration: 0 ? 1 Population prevalence of the disease: 0.3 ? .1 Genetic attributable fraction of the gene: 0.1 ? .05 Genetic model: ================= Model: Add=0 Multi=1 Recessive=2 Dom=3: 2 Allele frequency of the disease allele: 0.1 Population prevalence of the disease: 0.1 Genetic attributable fraction of the allele: 0.05 Penetrance for AA: 0.595 Penetrance for AB: 0.095 Penetrance for BB: 0.095 Relative Risk RR1: 1 Relative Risk RR2: 6.263 Odds ratio OR1: 1 Odds ratio OR2: 14 Allelic odds ratio: 1.616 Allele frequency of the marker gene: 0.1 P(Disease allele A| Marker allele A): 1 D' : 1 (0) Return to main menu (1) Specify genetic model based on MOI, p, K & AF (2) Specify genetic model based on penetrance values & allele frequency (3) Specify genetic model based on MOI, p, K & odds-ratio (4) Specify genetic model based on MOI, p, K & allelic odds-ratio 0 ? 0 Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 3 Statistical parameters: ====================== Significance level: 0.01 ? Offset : 0.1 ? Any key to clear screen Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 4 Computation method : ==================== 1=numerical integration, 2=approximation, 3=simulation: 1 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 other parameters: ================= Allele frequency of the disease gene: 0.1 Population prevalence of the disease: 0.1 Genetic attributable fraction of the gene: 0.05 Penetrance for AA: 0.595 Penetrance for AB: 0.095 Penetrance for BB: 0.095 Relative Risk RR1: 1 Relative Risk RR2: 6.263 Odds ratio OR1: 1 Odds ratio OR2: 14 Allelic Odds ratio: 1.616 Offset: 0.1 Significance level: 0.01 Computation based on numerical integration AF=0.05 Allele freq: 0.1 Power: 0.8168 Any key to clear screen Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 4 Computation method : ==================== 1=numerical integration, 2=approximation, 3=simulation: 2 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 other parameters: ================= Allele frequency of the disease gene: 0.1 Population prevalence of the disease: 0.1 Genetic attributable fraction of the gene: 0.05 Penetrance for AA: 0.595 Penetrance for AB: 0.095 Penetrance for BB: 0.095 Relative Risk RR1: 1 Relative Risk RR2: 6.263 Odds ratio OR1: 1 Odds ratio OR2: 14 Allelic Odds ratio: 1.616 Offset: 0.1 Significance level: 0.01 Computation based on approximation AF=0.05 Allele freq: 0.1 Power: 0.8368 Any key to clear screen Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 4 Computation method : ==================== 1=numerical integration, 2=approximation, 3=simulation: 3 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 other parameters: ================= Allele frequency of the disease gene: 0.1 Population prevalence of the disease: 0.1 Genetic attributable fraction of the gene: 0.05 Penetrance for AA: 0.595 Penetrance for AB: 0.095 Penetrance for BB: 0.095 Relative Risk RR1: 1 Relative Risk RR2: 6.263 Odds ratio OR1: 1 Odds ratio OR2: 14 Allelic Odds ratio: 1.616 Offset: 0.1 Significance level: 0.01 Computation based on simulation AF=0.05 Allele freq: 0.1 Power: 0.8169 Any key to clear screen Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? 4 Computation method : ==================== 1=numerical integration, 2=approximation, 3=simulation: 3 Family design: =============== (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring phenotyped # offspring: 1 # missing parents: 0 # families: 213 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 2 # missing parents: 2 # families: 220 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 1 # families: 175 (*) Ascert| proband 1: affected proband 2: unknown Addditional offspring not phenotyped # offspring: 3 # missing parents: 2 # families: 220 other parameters: ================= Allele frequency of the disease gene: 0.1 Population prevalence of the disease: 0.1 Genetic attributable fraction of the gene: 0.05 Penetrance for AA: 0.595 Penetrance for AB: 0.095 Penetrance for BB: 0.095 Relative Risk RR1: 1 Relative Risk RR2: 6.263 Odds ratio OR1: 1 Odds ratio OR2: 14 Allelic Odds ratio: 1.616 Offset: 0.1 Significance level: 0.01 Computation based on simulation AF=0.05 Allele freq: 0.1 Power: 0.8182 Any key to clear screen Power calculations for family-based association test (for binary traits) ======================================================================== (1) Design: Family-types, sample sizes and ascertainment condition (2) Genetic model (3) Statistical parameters (4) Power computation (-1) Exit 0 ? -1
Documentation
http://www.biostat.harvard.edu/%7Eclange/default.htm
