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Error No File Plink.fam Exists


Variant Call Format --vcf [filename] --bcf [filename] --vcf loads a (possibly gzipped) VCF file, extracting information which can be represented by the PLINK 1 binary format and ignoring everything else (after Convert .Pre Files To .Ped And .Map Files For Plink Hello, For association studies, I have the genotype data in .pre, .dat and .map (pre make-ped fo... plink --file data --extract myrange.txt --range

All SNPs within that range will then be excluded or extracted. To actually create a 'NA' cluster (this is PLINK 1.07's behavior), use the 'keep-NA' modifier. --loop-assoc [filename] Given a cluster file, this runs each specified case/control association command once for

When using PLINK on a machine with no, or a very slow, web connection, it may be desirable to turn this feature off. ADD REPLY • link written 5.3 years ago by Zhshqzyc • 370 [code]Ignore it. Imputed genotypes will be set to missing (i.e. A file formatted in this way can load into Excel, for example, as a tab-delimited file, but with one genotype per column instead of one allele per column.

Plink Fam File

If this were 10001 1 P1 10002 1 P1 10003 1 P2 10004 1 P2 10005 1 P3 10006 1 P3 ... Report postprocessing --annotate --clump --gene-report --meta-analysis Epistasis --fast-epistasis --epistasis --twolocus Allelic scoring (--score) R plugins (--R) Secondary input GCTA matrix (.grm.bin...) Distributed computation Command-line help Miscellaneous Tabs vs. Hi Everyone, I am trying to build a random forest classifier for a 6K microarray data. different to "plink") by using the --out option: plink --file mydata --out mydata --make-bed

which will create mydata.bed mydata.fam mydata.bim To subsequently load a binary file, just use --bfile instead

However, to maintain backwards compatibility with PLINK 1.07, PLINK 1.9 normally forces major alleles to A2 during its loading sequence. Avoid them. They're irrelevant unless you are merging with a dataset which contains known relatives. Plink Manual Post Reply Print view Search Advanced search 4 posts • Page 1 of 1 teb Posts: 2 Joined: Mon Jan 14, 2013 10:33 pm readin PLINK files with extensions .bed, .bim,

Write covariate files

If a covariate file is specified along with any of the above --recode options or with --make-bed, then that covariate file will also be written, as plink.cov Plink Merge Remove Duplicate Individuals From Plink Ped File Using Plink I have a plink ped file. In some cases the error may have more parameters in Error No File Plink.fam Exists format .This additional hexadecimal code are the address of the memory locations where the instruction(s) was If this is the case, a message will be written to the LOG file.

If any sample ID does not contain exactly one instance of the delimiter, an error is normally reported; however, if you have simultaneously specified --double-id or --const-fid, PLINK will fall back Plink Vcf Population stratification --cluster --pca --mds-plot --neighbour Association analysis Basic case/control (--assoc, --model) Stratified case/control (--mh, --mh2, --homog) Quantitative trait (--assoc, --gxe) Regression w/ covariates (--linear, --logistic) --dosage But all the necessary fields are there in different columns. To make a set file of all SNPs not in the specified ranges, add --make-set-complement-all SETNAME Optionally, the range file can contain a fifth column, to specify groups of ranges.

Plink Merge

Multimarker tests Imputing haplotypes Precomputed lists Haplotype frequencies Haplotype-based association Haplotype-based GLM tests Haplotype-based TDT Haplotype imputation Individual phases 16. specified by --file or --ped. Plink Fam File All generated samples are females with random genotype and phenotype values. --pheno In Plink Genotypes not in the this file will be untouched.

This could cause a problem if the file has been filtered, etc. shekhar_ssm Shell Programming and Scripting 0 03-16-2008 01:35 PM All times are GMT -4. PLINK 1.9 index... This option is useful if the covariate file has a different number of individuals, or is ordered differently, to produce a set of covariate values that line up more easily with Plink Allele Frequency

If a person is in the alternate phenotype file but not in the original file, that entry will be ignored. 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). If both --set-names and --subset are present, all sets named in either list are loaded. Permutation procedures Basic permutation Adaptive permutation max(T) permutation Ranked permutation Gene-dropping Within-cluster Permuted phenotypes files 14.

For example, plink --bfile mydata --snps rs273744-rs89883,rs12345-rs67890,rs999,rs222

selects the same range as above (rs273744 to rs89883) but also the separate range rs273744 to rs89883 as well as the two individual Plink Update Phenotype After checking, PLINK writes a file called .pversion to the working directory and use this cached information for the rest of the day. A8504 1 5 0.606218 A8008 1 1 0.442154 A8542 1 7 0.388042 A8022 1 2 0.286125 A8024 1 3 0.903004 A8026 1 4 0.790778 A8524 1 -9 0.713952 A8556 1 0

Use --make-bed for this.


In this case, the majority of alleles will be the reference, and so need not be repeated here. Based on multiple SNPs and ranges (--snps) Alternatively, the newer --snps command is more flexible but slower than the previously described --snp and --from/--to commands. PLINK will give an error message in most circumstances when something has gone wrong. … which implies mydata.tped and mydata.tfam exists; … ( binary file, genotype information ) plink.fam … ERROR: Plink Tutorial Of particular interest is when one SNP shows a large number of NEG SNPs.

All SNPs (whether haploid or not) must have two alleles specified. Remove a subset of individuals

To remove certain individuals from a file plink --file data --remove mylist.txt

where the file mylist.txt is, as for the --keep command, just a 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. No header row should be given.

Alternate phenotype files

To specify an alternate phenotype for analysis, i.e. Transposed genotype files When using either --recode or --recode12, you can obtain a transposed text genotype file by adding the --transpose option. Disclaimer: This website is not affiliated with Wikipedia and should not be confused with the website of Wikipedia, which can be found at Wikipedia.org. File formats...

The paternal ID and maternal ID are set to missing by default. How to easily fix Error No File Plink.fam Exists error? Due to how the PLINK 1 binary fileset format is defined, they cannot contain spaces3. The system returned: (22) Invalid argument The remote host or network may be down.

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 GT 0/0 ./. ./. 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 The 23andMe file format also does not always mark the boundaries of the X chromosome pseudo-autosomal region, so PLINK does not convert the chromosome code for 2-allele markers on male X

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 Update allele information

To recode alleles, for example from A,B allele coding to A,C,G,T coding, use the command --update-alleles, for example ./plink --bfile mydata --update-alleles mylist.txt --make-bed --out newfile

Rare CNVs File format MAP file construction Loading CNVs Check for overlap Filter on type Filter on genes Filter on frequency Burden analysis Geneset enrichment Mapping loci Regional tests Quantitative traits Command reference table

List of options List of output files Under development 5.

The file format is the same as for --pheno (optional header line, FID and IID in first two columns, covariates in remaining columns).