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Before we can create the PLINK command line you require, we need to gather some further details regarding filenames and some specific parameter values.
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Input files

--file > PED and MAP root file name. e.g. use this if the PED and MAP file have the same file root, e.g. entering data implies data.ped and data.map
OR
--ped > PED file name. Individually specify the full PED file, i.e. including any .ped extension, for example.
--map > MAP file name. Individually specify the MAP file, i.e. including any .map extension, for example.
--bfile > Binary PED file names. e.g. use this if you BED, BIM and FAM files with the same name, data.bed, data.bim and data.fam exist. These files are created by the --make-bed (create binary PED file) option.
OR
--bed > BED file name. The name of the binary PED (BED) file, which contains genotype information in a compressed format.
--map > BIM file name. This specifies the binary format MAP file.
--fam > FAM file name. This file is equivalent to the first six columns of a PED file, containing family and individual IDs and sex and phenotype information.

Output files

--out > Root output file name. All output files will begin with this root name, e.g. if you enter proj1 then files proj1.log, proj1.freq, etc.

Missing Values

These parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
> onclick=GrayOut(this,"missg","0","ch_missg")> --missing -genotype > Missing genotype value. The default missing genotype value is 0.
> onclick=GrayOut(this,"missp","-9","ch_missp")> --missing -phenotype > Missing phenotype value. The default missing phenotype value is -9.

Alternate phenotype files

These parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
> onclick=GrayOut(this,"pheno","","ch_pheno")> --pheno > Phenotype file name. File containing three columns: family ID, individual ID and phenotype.
> onclick=GrayOut(this,"mpheno","","ch_mpheno")> --mpheno > Phenotype column. If the file in --pheno has multiple phenotype columns, enter the desired column here. For example, to use the second phenotype, enter 2. (Optional)

Threshhold value filtering

These parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
> onclick=GrayOut(this,"mind","0.1","ch_mind") > --mind > Individual missing genotyping threshold. Individuals with more than this proportion of missing genotypes will be excluded from analysis. A list of these individuals is saved in the *.irem file.
> onclick=GrayOut(this,"geno","0.1","ch_geno")> --geno > SNP missing genotyping threshold. SNPs with more than this proportion of missing genotypes will be excluded (calculated after removing individuals).
> onclick=GrayOut(this,"maf","0.01","ch_maf")> --maf > Minor allele frequency. SNPs with a minor allele frequency less than this will be excluded from analysis (based on founders only, after removing individuals with high missing rates).
> onclick=GrayOut(this,"cell","5","ch_cell")> --cell > Minimum cell count for genotypic analysis. SNPs with any cell with fewer than this many genotypes in the 2x3 genotypic table (--model option) are not included in the genotypic analysis.
> onclick=GrayOut(this,"hwe","0.001","ch_hwe")> --hwe > Hardy-Weinberg test p-value. SNPs that show departure from HWE with p-values less than this value will be excluded.
> onclick=GrayOut(this,"ime","0.1","ch_me");GrayOut(this,"fme","0.1","ch_me")> --me >
>
Mendel error rate thresholds (per SNP, per family). SNPs that show in more than this proportion of informative transmissions will be excluded; the second threshold more Mendel error departure from HWE with p-values less than this value will be excluded.

SNP Location filtering

These parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
>
> onclick=GrayOut(this,"chr","","ch_chr")> --chr > Select chromosome. Enter chromosome from which to pick SNPs.
OR
onclick=GrayOut(this,"from","","ch_loc");GrayOut(this,"to","","ch_loc")> --from
--to
>
>
Select range of SNPs Enter two SNP IDs. This selects the SNPs from the SNP ID listed in --from to the SNP ID listed in --to. Both SNP IDs must be on a single chromosome.

Merge fileset parameters

--merge >
>
Full PED and MAP filenames. Specify the new to-be-merged-in fileset here; include any .ped and .map extensions.
--merge -mode > 1
> 2
> 3
> 4
> 5
> 6
> 7
Merge mode. This option specifies the behavior of the --merge option, as described in the main documentation page. Briefly: 1) consensus (default); 2) Only overwrite calls which are missing in original; 3) Only overwrite calls which are not missing in new file; 4) Never overwrite; 5) Always overwrite; 6) Report all matching calls (diff mode -- do not merge); 7) Report mismatching non-missing calls (diff mode -- do not merge)

Merge multiple filesets

--merge-list > List of to-be-merged PED and MAP files. Each line should contain a pair of PED and MAP files, as described in the documentation. These files will be merged into the input file listed above.

List of SNPs to extract

--extract > Filename of list of SNPs to extract. This file should just contain a list of SNP IDs, one per line.

List of SNPs to exclude

--exclude > Filename of list of SNPs to exclude. This file should just contain a list of SNP IDs, one per line.

List of individuals to extract

--keep > Filename of list of individuals to extract. This file should just contain a list with one individual per line, each line has two columns: family ID and individual ID which should uniquely identify a person.

List of individuals to exclude

--remove > Filename of list of individuals to exclude. This file should just contain a list with one individual per line, each line has two columns: family ID and individual ID which should uniquely identify a person.

List of SNPs to flip strand

--flip > Filename of list of SNPs to flip strand. This file should just contain a list of SNP IDs, one per line.

IBS clustering parameters

--ppc > Pairwise population test threshold. Do not pair individuals in the clustering procedure who have a p-value more significant than this in the binomial pairwise population test. These p-values are available for pairs by using the --genome option.
OR
--matrix > onClick=HidCheck(this,"ch_matrix") > Output IBD distance matrix. If this box is checked, then the matrix of pairwise IBD distances will be generated, called *.mdist

Case-control clustering

These parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
--mcc > > Maximum case/controls The maximum number of cases and the maximum number of controls per cluster. (Optional)
OR
--mc > Maximum cluster size The maximum number of individuals in each cluster. (Optional)
--cc > onClick=HidCheck(this,"ch_cc") > Case/control Require at least one case and one control in each cluster. (Optional)

External matching criteria

--match > File name of categorical matching file. This file contains family ID and individual ID as the first two columns: subsequent columns define whether two individuals can be matched.
> onclick=GrayOut(this,"matchtype","","ch_matchtype") > --match-type > File name of categorical matching direction definition file. This optional file contains a series of flags, one per categorical matching variable, that indicate whether the match should be positive (+ or 1) or negative (- or 0). That is, this determines whether we allows only individuals with similar (positive) or dissimilar (negative) values for the categorical matching criterion. (Optional)
OR
--qmatch > File name of quantitative trait matching file. This file contains family ID and individual ID as the first two columns: subsequent columns define whether two individuals can be matched.
--qt > File name of quantitative trait thresholds. The file specifies the threshold for each quantitative matching criteria that defines a match or mismatch. e.g. a value of 5 means that only individuals who differ by 5 or less units on that criterion can be matched.

Pairwise genome-wide IBD comparisons

--min > Minimum pi-hat to output pair. The --genome option considers all pairs of individuals: with large samples this can generate very large files. To only output pairs that show IBD above a certain level, use this option, i.e. 0.01 implies pairs that share 1% of their genome or more; pi-hat is P(IBD=2) + P(IBD=1)/2

Defining stretches of homozygosity

--homo-run-snps > Number of consecutive SNPs required to define a homozygous stretch. Future implementations will allow for genotyping error to break homozygous stretches and allow for physical distance thresholds.

Pairwise SNP/SNP linkage disequilibrium

--r
--r2
>
>
Measure of pairwise LD. Specify either the basic correlation coefficient (top button) or the squared coefficient (bottom button). Both measures are calculated from the unphased genotype data.

Haplotype inference / multimarker predictors

--hap > Filename of haplotype definition list. This file, described in the main documentation, contains the haplotypes to be inferred.
--pp > Posterior probability phase threshold. When imputing alleles based on the most likely haplotype, a missing call will be made if the most likely phase is less likely than the threshold specified here.

max(T) Permutation

--mperm > Number of Permutations Number of permutations to run when in max(T) mode.

Homogeneity of Odds Ratios Tests

--bd
--homog
>
>
Select Odds Ratio Test The --bd option selects a "Breslow-Day" homogeneity of odds ratios test and the --homog option selects a "Partitioning chi-square" homogeneity of odds ratios test.

Clustering

--within > Read cluster definitions from a file for stratified analyses. This file should contain three columns: family ID and individual ID followed by the cluster code for that individual.
OR
--family > onClick=HidCheck(this,"ch_family") > Cluster based on families. This option uses family ID to define clusters, as used in various stratified analyses and permutation procedures.

Family-based association (TDT)

--tdt
--parentdt1
--parentdt2
>
>
>
TDT or parenTDT statistic to be used for permutation. These options specify which statistic is used to generate empirical p-values (reported in the *.perm.tdt file: basic TDT, parental discordance test, combined TDT and parental discordance test.

Covariate File

--covar > Covariate file name. File containing three columns: family ID, individual ID and covariate.
OR
--mcovar > Multiple covariate file name. File containing at least three columns: family ID, individual ID and at least one covariate.
> Covariate column. Select the nth covariate.

SNP x SNP epistasis

--epi1 > Threshold (p-value) for reporting a result Testing all pairs of SNPs for epistasis can generate very large output files if there are very many SNPs: this option is used to only output tests (to the *.epi-cc1 or *.epi-co1 files) that are significant at the specified level.
--epi2 > Threshold (p-value) for summarising results For the the *.epi-co2 and *.epi-cc2 files, this option defines a significant epistatic result.
> N by N
> S by S
> S by N
> S1 by S2
Mode for epistatic SNP x SNP tests. If there are N SNPs in total; an optional set file may either contain 1 or 2 sets. This option determine whether and how sets are used to select epistatic tests. The first option does not require any sets; the second and third option require a set file with a single set; the fourth option requires a set file with exactly two sets.
--set > Set filename to define epistatic tests If you are using sets to define which pairs of SNPs to test for epistasis, specify the filename here, otherwise this can be left blank. See the main documentation for details.

Gene-based epistasis

--mperm > Number of permutations to perform. Currently, the gene-based test relies on permutation to generate empirical significance levels. This test is computationally intensive -- it might not be feasible to test a large number of genes with a large number of permutations. Future versions will adopt a more efficient gene-based testing procedure.

max(T) Permutation

--mperm > Number of Permutations Number of permutations to run when in max(T) mode.

Set-based tests

Some of parameters are optional. To change a value, check the box on the right and enter a new value. If no value is given, the default will be used.
--set > Set file You must specify a set file with one or more sets, idenitify the SNPs for each set. See the main documentation for details.
> onclick=GrayOut(this,"setmin","1","ch_setmin") > --set-min > Minimum set size This parameter indicates the minimum number of SNPs used in the rank-sum test.
> onclick=GrayOut(this,"setmax","n/a","ch_setmax") > --set-max > Maximum set size This parameter indicates the maximum number of SNPs used in the rank-sum test (default is the number of SNPs in the set).

 

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