–make-just-bim is actually a variation out of –make-bed which simply makes a .bim file, and you will –make-just-fam takes on the same role to possess .fam documents. Instead of most other PLINK sales, this type of not one of them the main enter in to include a beneficial .sleep file ( you won’t have entry to many selection flags while using the this type of during the zero-.bed function).
Use these very carefully. It is rather simple to desynchronize your binary genotype research and you can their .bim/.fam indexes by using this type of instructions badly. For those who have question, follow –make-bed.
Create text fileset
–recode creates a separate text fileset, immediately following implementing take to/version strain or any other functions. Automatically, the fileset comes with a good .ped and a good .map file, viewable with –file.
- The ’12’ modifier causes A1 (always lesser) alleles is coded as ‘1’ and you will A2 alleles getting coded just like the ‘2’, if you are ’01’ charts A1>0 and you will A2>1. (PLINK pushes one to merge ’01’ having –[output-]missing-genotype when this is needed to prevent missing genotypes off become indistinguishable out-of A1 phone calls.)
- This new ’23’ modifier causes an excellent 23andMe-formatted document are generated. This may simply be put on a single sample’s data (a-one-line –keep file can come for the convenient here). Discover already zero special handling of the new XY pseudo-autosomal part.
- Brand new ‘AD’ modifier grounds an ingredient (0/1/2) + dominant (het = step 1, otherwise 0) part document, suitable for loading out-of R, getting produced. ‘A’ is the identical, except without having any dominance component.
- Automagically, A1 alleles is actually mentioned; this might be designed that have –recode-allele. –recode-allele’s enter in file need to have version IDs in the 1st column and you may allele IDs regarding second.
- Automagically, the heading line to have .brutal records merely names the brand new counted alleles. To include the solution allele rules too, range from the ‘include-alt’ modifier.
- Haploid additive components is 0/2-valued as opposed to 0/1-cherished, to maintain a routine level to your X-chromosome.
Irregular efficiency programming
g. ’23’ to own human X. –output-chr enables you to specify a new programming scheme by giving the new need individual mitochondrial code; served choices are ’26’ (default), ‘M’, ‘MT’, ‘0M’, ‘chr26’, ‘chrM’, and you will ‘chrMT’. (PLINK step one.nine precisely interprets each one of these encodings when you look at the enter in documents.)
–output-missing-genotype makes you replace the reputation (normally the –missing-genotype value) accustomed show forgotten genotypes within the PLINK productivity data, whenever you are –output-missing-phenotype transform this new string (often the –missing-phenotype worthy of) representing lost phenotypes.
Observe that such flags don’t affect –[b]merge/–merge-record or perhaps the autoconverters, because they generate data files that age focus on. Incorporate –make-bed if you want to change missing genotype/phenotype programming when doing those individuals businesses.
Lay reduces off genotype phone calls to help you forgotten
If the groups was outlined, –zero-class takes a document with version IDs in the 1st column and you can class IDs in the next, and you can kits the involved genotype calls to help you missing. See the PLINK step one.07 files to possess an illustration.
It flag need to today be used which have –make-sleep without almost every other output requests (as the PLINK no longer has the complete genotype matrix in memories).
Heterozygous haploid errors
Generally speaking, heterozygous haploid and you may nonmale Y chromosome genotype calls was logged to plink .hh and treated just like the missing by the most of the analysis sales, but leftover undisturbed by the –make-bed and you will –recode (because, shortly after sex and you will/otherwise chromosome code problems was fixed, the fresh phone calls usually are appropriate). For individuals who in reality require –make-bed/–recode to help you delete this information, have fun with –set-hh-forgotten. (The new range from the flag is a little greater than for PLINK 1.07, since the requests particularly –checklist and –recode-rlist and therefore in the past failed to admiration –set-hh-lost had been consolidated lower than –recode.)
Keep in mind that the most used supply of heterozygous haploid errors are brought in investigation and therefore will not pursue PLINK’s meeting to own symbolizing the new X chromosome pseudo-autosomal part. This should be given –split-x lower than, not –set-hh-lost.