MultiSV: MultiSV: an R package for identification of structural variations in multiple populations based on whole genome resequencing

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MultiSV is an R package for identification of structural variations in multiple populations based on whole genome resequencing. It fits linear mixed model and identifies structural variations in multiple populations using whole genome sequencing data. It could also be manipulated to use on RNA-seq data for differential gene expression (implementation in future releases). Main steps for analysis include generating read depth in bins using ComputeBinCounts. conversion of bins to MultiSV format using Bin2MultiSV. Finally, identification of structural variations using CallMultiSV.

Author
Khurram Maqbool
Date of publication
2014-08-27 18:52:26
Maintainer
Khurram Maqbool <khurram.maqbool@outlook.com>
License
LGPL (>= 3)
Version
0.0-67

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Man pages

Bin2MultiSV
Read data using configuration file
CallMultiSV
A Method to identify MultiSV from RDbin files for different...
CmptMltPvl
Compute Pvals of MultiSVs
ComputeBinCounts
Compute read counts in bins from read hits.
GetTestCfgFile
Function with MultiSV input example
gtExEs
proc information
IdfMltSV
Call MultiSVs
MultiSVData
RD Data
MultiSVExample
MultiSV Example
PrbMlt
Fit linear mixed model
PrepMultiDt
Prepare MultiSV data
PrepMultiDtLgMn
Prepare MultiSV data
ProcMutilDt
Process Multi Data
WriteMultiSV
Output MultiSVs

Files in this package

MultiSV
MultiSV/inst
MultiSV/inst/RPRL
MultiSV/inst/RPRL/Hits2MultiSVBin
MultiSV/inst/CITATION
MultiSV/inst/extdata
MultiSV/inst/extdata/MultiSV.conf
MultiSV/NAMESPACE
MultiSV/data
MultiSV/data/datalist
MultiSV/data/MultiSV.Data.rda
MultiSV/R
MultiSV/R/MultiSVP.R
MultiSV/R/MultiSVInDt.R
MultiSV/R/MultiSV.demo.R
MultiSV/R/MultiSVPrb.R
MultiSV/R/MultiSVOg.R
MultiSV/R/MultiSVHt2bn.R
MultiSV/R/MultiSVPrepareDt.R
MultiSV/R/MultiSV.example.R
MultiSV/R/MultiSVCl.R
MultiSV/R/MultiSVMn.R
MultiSV/R/MultiSVExe.R
MultiSV/R/MultiSVPrepareDtLgMn.R
MultiSV/R/MultiSVPrsDt.R
MultiSV/R/MultiSVIO.R
MultiSV/MD5
MultiSV/DESCRIPTION
MultiSV/man
MultiSV/man/MultiSVData.Rd
MultiSV/man/Bin2MultiSV.Rd
MultiSV/man/CmptMltPvl.Rd
MultiSV/man/MultiSVExample.Rd
MultiSV/man/gtExEs.Rd
MultiSV/man/PrepMultiDt.Rd
MultiSV/man/ComputeBinCounts.Rd
MultiSV/man/IdfMltSV.Rd
MultiSV/man/PrbMlt.Rd
MultiSV/man/PrepMultiDtLgMn.Rd
MultiSV/man/WriteMultiSV.Rd
MultiSV/man/ProcMutilDt.Rd
MultiSV/man/CallMultiSV.Rd
MultiSV/man/GetTestCfgFile.Rd