Exports genotypic data for QTL analysis (D.A. Murray).
Options
OUTFILENAME = text |
Name of the file to receive the data |
|---|---|
MAPFILENAME = text |
Name of the associated map file for Flapjack or MapQTL(R) |
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP, AMP); must be set |
NGENERATIONS = scalar |
Number of generations for a RIL population |
NAME = text |
Name for the header in a .loc file |
MISSING = text |
Character to represent a missing genotype in Flapjack or R/QTL format; default '-' |
SEPARATOR = text |
Character to separate data values in Flapjack format; default separates them by tabs |
ASEPARATOR = text |
Character to separate allele values in Flapjack format; default '/' |
FJROWS = string token |
Specifies whether the genotypes or markers are to be stored on the rows in Flapjack format (genotypes, markers); default geno |
Parameters
MKSCORES = pointers |
Genotype codes for each marker |
|---|---|
CHROMOSOMES= factors |
Linkage groups for the markers |
POSITIONS = variates |
Positions within the linkage groups of markers |
MKNAMES = texts |
Marker names |
MKSETS = factors |
Marker sets |
IDMGENOTYPES = texts |
Labels for genotypes |
PARENTS = pointers |
Parent information |
IDPARENTS = texts |
Labels used to identify the parents |
Description
QEXPORT saves genotypic map data for QTL analysis. The data are saved to the file specified by the OUTFILENAME option. The format of the file is specified by the file extension, and can be either a Flapjack text genotype file (.txt), a MapQTL(R) Locus genotype file (.loc) or an R/QTL separate genotype file (.csv). If a Flapjack genotype file or a MapQTL(R) Locus genotype file name is supplied, the associated map information can be saved by setting the MAPFILENAME option to a file name with the extension .txt for Flapjack or .map for MapQTL(R). QEXPORT can thus be used to save data in Flapjack format to use with the QIBDPROBABILITIES procedure.
The type of population must be specified using the POPULATIONTYPE option. The genotypic data can be exported for F2, first generation backcross (BC1), recombinant inbred lines (RIL) and DH1 (double-haploid) populations to any of the file types. The BCxSy (backcross inbred lines), CP (cross pollinator) and AMP (association mapping) populations can be exported only using the Flapjack format. If a RIL population is being exported to MapQTL(R), the number of generations should be specified using the NGENERATIONS option. Also, for exporting to MapQTL(R), the NAME option allows you to include a name for the population (which must not contain spaces).
The marker scores should be supplied in a pointer to a set of factors using the MKSCORES parameter. Each factor within the pointer should contain data for a marker, where the same factor labels are supplied in the same order. For the BC1, DH1, F2, RIL, BCxSy and CP populations, the parent information can be supplied in a pointer to a set of texts using the PARENTS parameter. Note that the PARENTS parameter must be set for a CP population. Each text should contain the parent allele, where the position within the pointer determines the parent: for example, the first text represents parent 1, the second text parent 2 and so on. For the BC1, DH1, F2, RIL and BCxSy populations, if the PARENTS parameter is not set, then the parent information is automatically generated where parent 1 is allocated allele 1 and parent 2 is allocated allele 2. The labels for the parents can be supplied in a text using the IDPARENTS parameter.
By default, in Flapjack or R/QTL files, missing alleles are represented using the '-' character, but an alternative can be supplied using the MISSING option. In Flapjack genotype files, the separator used between marker genotype scores can be supplied using the SEPARATOR option, and the separator used between alleles using the ASEPARATOR option. For the Flapjack genotype format, the FJROWS option indicates whether the genotypes or markers are stored in the rows of the file; by default the genotypes are in the rows.
The linkage groups for each marker are supplied in a factor by the CHROMOSOMES parameter. The names of the markers are supplied in a text using the MKNAMES parameter, and the marker positions are supplied in a variate using the POSITIONS parameter. For the .csv file format, a grouping factor identifying marker sets can be supplied using the MKSETS parameter.
The genotype labels to be stored in a Flapjack or R/QTL file can be specified using the IDMGENOTYPES parameter. If this parameter is not set, the labels will be generated automatically using the values 1 to n, where n is the number of genotypes.
Options: OUTFILENAME, MAPFILENAME, POPULATIONTYPE, NGENERATIONS, NAME. MISSING, SEPARATOR, ASEPARATOR, FJROWS.
Parameters: MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, MKSETS, IDMGENOTYPES, PARENTS, IDPARENTS.
Method
The .csv file format uses an extended version of the R/QTL comma-delimited separate file for genotype data (.csvsr and .csvs), where there is an optional column for marker sets. For exporting large data sets to .csv format, the procedure uses the Dataload.dll library. In the .csvsr file format, the first row specifies the genotype or id, and there must be a column of data associated with the phenotypic data with exactly the same information. The first cell should be the name of an identifier for the genotype id, and the first row in columns 2 and 3 should be blank. Also, if marker sets are included in the file, the first row of column 4 should be left blank. Starting from row 2 in the file, the first column gives the marker names, the second column gives the linkage group for each marker, and the third column gives the positions of the markers within the linkage groups. The fourth column can be used to contain the marker sets. The remaining columns give the marker genotypes.
Action with RESTRICT
All restrictions are ignored.
See also
Procedures: EXPORT, QIMPORT, QIBDPROBABILITIES.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QEXPORT example'; STYLE=meta
QIMPORT [POPULATION=F2] FILENAME='%GENDIR%/Examples/F2maize.loc';\
MAPFILENAME='%GENDIR%/Examples/F2maize.map';\
MKSCORES=mgenotypes; CHROMOSOMES=linkagegroups;\
POSITIONS=lpos; MKNAMES=markers; IDMGENOTYPES=idmgenotypes;\
PARENTS=parents; IDPARENTS=idparents
" Export to Flapjack format "
QEXPORT [OUTFILENAME='F2maize_genoExport.txt';\
MAPFILENAME='F2maize_mapExport.txt';\
POPULATION=F2] MKSCORES=mgenotypes; CHROMOSOMES=linkagegroups;\
POSITIONS=lpos; MKNAMES=markers; IDMGENOTYPES=idmgenotypes;\
PARENTS=parents; IDPARENTS=idparents
" Export to R/QTL rotated separate genotype file "
QEXPORT [OUTFILENAME='F2maizeExport.csv'; POPULATION=F2] MKSCORES=mgenotypes;\
CHROMOSOMES=linkagegroups; POSITIONS=lpos; MKNAMES=markers;\
IDMGENOTYPES=idmgenotypes; PARENTS=parents; IDPARENTS=idparents