Class | Analysis and data manipulation command |
Name | keep | drop |
Arguments | <loc1>...[<locB> to<locC>]... [$(m|x|h|q|a)]...<locN>. |
Retain or exclude loci for subsequent analysis. Consecutive loci can be summarized as a range, as can all members of a particular class of locus type (marker, quantitative, affection) via a class ($type) token. Note that dropped variables can still be used in some algebraic and logical expressions.
Example:
>> include volgaex.in >> keep D14S* Keeping 3 active loci.
Class | Analysis and data manipulation command |
Name | keep | drop |
Arguments | where (monomorphic | diallelic | allele_number [<c_op>] <numal> | spectrum <allele1-allele2-...alleleN> | max [<|<=|>|>=|==|^=] <frequency> | number_typed [<|<=|>|>=|==|^=] (<ntyp>| <prop_typ>) | missing [<|<=|>|>=|==|^=] (<ntyp>| <prop_typ>) | distance <smallest_gap> | chromosome <chr1> [...<chrN>] | position <start_of_interval> <end_of_interval> | near <locus> [...<locusN>] [<set_size>] | r2 <largest_r2> | every number_skipped | hwe_p [<|<=|>|>=|==|^=] [<critical_P>] | test_p [<|<=|>|>=|==|^=] [<critical_P>] | covers <trait> [[<|<=|>|>=|==|^=]<] n_uncovered_cats>] | in <file> | <search_string>) |
Retain or exclude loci for analysis. Note that dropped variables can still be used in algebraic and logical expressions. The where condition can be used to match the set of loci meeting that condition. Available conditions are:
In the case of the r2 and distance options, keep and drop has the same effects, as it doesn't make sense to filter all SNPs that are distant from one another. One can use diseq <target> followed by drop where test to include or exclude all marker in LD with a given target marker.
The covers option is to find useful markers for comparing strata, where membership is indexed by a trait. Not infrequently, a particular marker may not have been genotyped for one or more subgroups in a study.
Example:
>> include volgaex.in >> keep where hwe Selecting markers with HWE P-value <= 0.016952427508441503 Keeping 1 active locus. >> undrop >> keep where spectrum 144-148-149-151-155-157 Selecting markers with allele spectrum "144-148-149-151-155-157" Keeping 1 active locus.
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