| Type: | Package |
| Title: | A BSA Software for Detecting All Types of QTLs in BC, DH, RIL and F2 |
| Version: | 1.0.2 |
| Maintainer: | Yuan-Ming Zhang <soyzhang@mail.hzau.edu.cn> |
| Contact: | Yuan-Ming Zhang <soyzhang@mail.hzau.edu.cn> |
| Description: | The new (dQTG.seq1 and dQTG.seq2) and existing (SmoothLOD, G', deltaSNP and ED) bulked segregant analysis methods are used to identify various types of quantitative trait loci for complex traits via extreme phenotype individuals in bi-parental segregation populations (F2, backcross, doubled haploid and recombinant inbred line). The numbers of marker alleles in extreme low and high pools are used in existing methods to identify trait-related genes, while the numbers of marker alleles and genotypes in extreme low and high pools are used in the new methods to construct a new statistic Gw for identifying trait-related genes. dQTG-seq2 is feasible to identify extremely over-dominant and small-effect genes in F2. Li P, Li G, Zhang YW, Zuo JF, Liu JY, Zhang YM (2022, <doi:10.1016/j.xplc.2022.100319>). |
| Depends: | R (≥ 3.5.0) |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Imports: | BB, data.table, doParallel, openxlsx, qtl, stringr, writexl,vroom, parallel,foreach |
| Encoding: | UTF-8 |
| LazyData: | true |
| Packaged: | 2023-03-21 09:51:30 UTC; Administrator |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Author: | Pei Li [aut],
Yuan-Ming Zhang 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2023-03-22 09:10:06 UTC |
BSA data
Description
BSA format of F2 dataset.
Usage
data(BSA)
Details
Input file for dQTG.seq function.
To perform method
Description
To perform method
Usage
Dodata(dir, calculatedata, chr, color1, CLO)
Arguments
dir |
the path of the output |
calculatedata |
the inputdata |
chr |
chromosome |
color1 |
the color of the chromosome |
CLO |
the numbers of CPU |
Value
list
Examples
data(BSA)
dir<- tempdir()
data.calculatedata<-Readdata1(BSA)
Dodata(dir,calculatedata=data.calculatedata,chr="all",color1="blue",CLO=1)
Title readdata function
Description
Title readdata function
Title readdata function
Usage
Readdata1(File)
Readdata1(File)
Arguments
File |
the input file |
Value
list
list
Examples
data(BSA)
Readdata1(BSA)
data(BSA)
Readdata1(BSA)
Title The function of dQTG.seq
Description
Title The function of dQTG.seq
Usage
dQTG.seq(dir, filegen, chr, color, CLO)
Arguments
dir |
the path of the output |
filegen |
the input data |
chr |
the chromosome |
color |
the color |
CLO |
the numbers of CPU |
Value
list
Examples
data(BSA)
dQTG.seq(dir=tempdir(),filegen=BSA,chr="all",color="blue",CLO=1)