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Error No File Plink.fam Exists


All generated samples are females with random genotype and phenotype values. To recode SNP alleles from A,C,G,T to 1,2,3,4 or vice versa, use --allele1234 (to go from letters to numbers) and --alleleACGT (to go from numbers to letters). The order of individuals in this file is the same as the order across the columns of the TPED file. if bigpheno.raw contains 10,000 phenotypes, then plink --bfile mydata --assoc --pheno bigpheno.raw --all-pheno

will loop over all of these, one at a time testing for association with SNP, generating a

other than the one in the *.ped file (or, if using a binary fileset, the *.fam file), use the --pheno option: plink --file mydata --pheno pheno.txt

where pheno.txt is a The name is followed by a list of SNPs in that set. plink --bfile mydata --make-pheno p1.list * --assoc

which assumes the file p1.list contains exactly two fields Family ID Individual ID In this case, anybody in the file p1.list would be options 21.

Plink Fam File

Disclaimer: This website is not affiliated with Wikipedia and should not be confused with the website of Wikipedia, which can be found at options 22. Consider this example file, Q A 1 rs1234 0.986 Q B 1 rs1234 0.923 Q A 1 rs5678 0.323 Q B 1 rs5678 0.97 that lists two genotypes for people with Miscellaneous Command options/modifiers Association output modifiers Different species Known issues 35.

The command to set the latter is --reference-allele {file}

Also note in this example, that a) when an individual is set as explicitly missing in the LGEN file, they stay Error in Snp set analysis using MetaSKAT Hello, I am tring to run MetaSkat on three cohorts and get the following error EX.set.bed<-... the changes are not automatically saved).

The file with new SNP information does not need to feature all of the SNPs in the current dataset: SNPs not in this file Plink Manual LD calculations 2 SNP pairwise LD N SNP pairwise LD Tagging options Haplotype blocks 15.

the same SNPs that a --recode or --make-bed statement would have produced in the corresponding MAP or BIM files. One must combine these options with the desired analytic (e.g. --assoc), summary statistic (e.g. --freq) or data-generation (e.g. --make-bed) option. Set files

Certain analyses (e.g. gPLINK gPLINK mainpage Tour of gPLINK Overview: using gPLINK Local versus remote modes Starting a new project Configuring gPLINK Initiating PLINK jobs Viewing PLINK output Integration with Haploview Downloading gPLINK

If you just want to convert your data, don't use any other flags besides --out. Plink Vcf For example, ./plink --bfile mydata --qual-scores myscores.txt --qual-threshold 0.8 --make-bed --out qc-data

where myscores.txt is a text file of SNPs and scores, e.g. If the 'tags' or 'haps' modifier is present, an extended nine-field simulation parameter file is expected instead: Number of SNPs in set Label of this set of SNPs Reference allele frequency The final mynewdata.* files will contain information from all 8 files.

The --merge-mode option can also be used with the --merge-list option, as described above: however, it is not possible

Plink Merge

Merge failures VCF reference merge --merge-list --write-snplist --list-duplicate-vars Basic statistics --freq{x} --missing --test-mishap --hardy --mendel --het/--ibc --check-sex/--impute-sex --fst Linkage disequilibrium --indep... --r/--r2 --show-tags --blocks Distance matrices Identity-by-state/Hamming (--distance...) Relationship/covariance Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » Home Plink Fam File FAQ & Hints

36. --pheno In Plink MAP files

By default, each line of the MAP file describes a single marker and must contain exactly 4 columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or

Chromosome codes The autosomes should be coded 1 through 22. An incomplete installation, an incomplete uninstall, improper deletion of applications or hardware. It can also be caused if your computer is recovered from a virus or adware/spyware attack or by an improper shutdown of the computer. It is sometimes useful to have a PED file that is tab-delimited, except that between alleles of the same genotype a space instead of a tab is used. Plink Allele Frequency

Rather than have a very large file, one could only list genotype scores that are below some threshold, for example, assuming most genotypes are of very good quality. But together with BED I... Q fam1 ind1 rs10001 0.873 Q fam1 ind1 rs10002 0.998 ... Novice Computer User Solution (completely automated): 1) Download (Error No File Plink.fam Exists) repair utility. 2) Install program and click Scan button. 3) Click the Fix Errors button when scan is

Of particular interest is when one SNP shows a large number of NEG SNPs. Plink Update Phenotype Note that --output-missing-phenotype can be given a nonnumeric string.) Case/control phenotypes are expected to be encoded as 1=unaffected (control), 2=affected (case); 0 is accepted as an alternate missing value encoding. Randomized data --dummy [sample count] [SNP count] {missing geno freq} {missing pheno freq} This tells PLINK to generate a simple dataset from scratch (useful for

Covariates --covar [filename] --covar-name [column ID(s)/range(s)...] --covar-number [column number(s)/range(s)...] --no-const-covar --allow-no-covars --covar designates the file to load covariates from.

ID helper Overview/example Basic usage Consistency checks Aliases Joint IDs Lookups Replace values Match files Quick match files Misc. 32. The family and within-family IDs default to 'FAM001' and 'ID001' respectively if you don't provide them. With a person wild-card, PLINK expects all quality scores for that SNP, in order as in the FAM or PED file, e.g. Plink Tutorial This happens before regular parsing, so when the --vcf-idspace-to and --id-delim characters are identical, both space and the original --id-delim character are interpreted as FID/IID delimiters.

If you only want

To merge all sets, use the --set-collapse-all flag. plink • 1.5k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 15 months ago by deepue • 60 • written 17 This command takes as a single argument the name of a file that lists SNP name and allele to report, e.g. If you have a header row, the first two variables must be labelled FID and IID.

You can specify another binary/continuous phenotype by name with --oxford-pheno-name. --hard-call-threshold [value] --hard-call-threshold random --missing-code {comma-separated list of values} (alias: --missing_code) Since the PLINK 1 binary format cannot represent genotype probabilities, setting the position to a negative value will not work to exclude a SNP for binary files

You can specify a different output root file name (i.e. The Error No File Plink.fam Exists error is the Hexadecimal format of the error caused. Alternatively, you can use --family to create a cluster for each family ID.

Gene-based report Basic usage Other options 24. Summary stats Missingness Obligatory missingness IBM clustering Missingness by phenotype Missingness by genotype Hardy-Weinberg Allele frequencies LD-based SNP pruning Mendel errors Sex check Pedigree errors 8.

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