xiaolei-lab/rMVP issues and pull requests

#97 - No PC or Kinship generated

Issue - State: open - Opened by ramendra-sarma 3 months ago

#96 - Question about PCA analysis

Issue - State: open - Opened by 1795106897 4 months ago

#95 - Manhattan plot

Issue - State: open - Opened by elissaralam 5 months ago

#94 - NA is not allowed in genotype, use 'MVP.Data.impute' to impute

Issue - State: open - Opened by suvihon 7 months ago - 1 comment

#93 - Fitting PCs with nPC vs CV

Issue - State: open - Opened by JandehF 8 months ago - 3 comments

#92 - A question about VCF format conversion

Issue - State: open - Opened by yuxizhang01 8 months ago - 3 comments

#91 - How can I calculate kinship matrix using the geno matrix?

Issue - State: open - Opened by bechee 8 months ago

#90 - Error in formatC(threshold/m, format = "e", digits = 2) : object 'n' not found

Issue - State: closed - Opened by Wyinghao 9 months ago

#89 - Error in make.names(col.names, unique = TRUE) : invalid multibyte string at '<ff><fe>I'

Issue - State: closed - Opened by Wyinghao 9 months ago - 2 comments

#88 - A question about FarmCPU

Issue - State: closed - Opened by z4668640 11 months ago - 3 comments

#87 - Can rMVP work on continuous genotype data?

Issue - State: open - Opened by White-Shinobi 11 months ago - 1 comment

#86 - PCA code given in the main pages only giving the 2D PCA, but image of 3D PCA plot is also given but its code is not provide, kindly please provide the code for 3D plot

Issue - State: open - Opened by krishna10597 about 1 year ago

#85 - Total 1 individuals removed due to missings Error in GetElements.bm(x, i, j) : Illegal column index usage in extraction. Calls: MVP -> [ -> [ -> .local -> GetElements.bm

Issue - State: open - Opened by kmosi0 about 1 year ago

#84 - ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'.

Issue - State: open - Opened by rupesht over 1 year ago - 1 comment

#83 - ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'.

Issue - State: open - Opened by rupesht over 1 year ago - 6 comments

#82 - Calculating PVE in rMVP

Issue - State: open - Opened by jhavill over 1 year ago - 1 comment

#81 - Error in analysing the all phenotype

Issue - State: open - Opened by ramendra-sarma over 1 year ago

#80 - Performing FarmCPU with iteraction between SNP

Issue - State: open - Opened by Mahounakpon almost 2 years ago - 2 comments

#79 - 表型分布

Issue - State: closed - Opened by MooreZhu about 2 years ago - 1 comment

#78 - using multiple cores

Issue - State: closed - Opened by MuBulut about 2 years ago - 3 comments

#77 - Problem in imMVP execution "Number of individuals in phenotype and genotype doesn't match"

Issue - State: open - Opened by Mahounakpon about 2 years ago - 5 comments

#76 - How to inport Q-matrix (from structure) to achieve Q+K mix module

Issue - State: closed - Opened by yiomoiy over 2 years ago - 2 comments

#75 - Unable to run rMVP Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nrow': object 'Phenotype' not found

Issue - State: open - Opened by rupesht over 2 years ago - 1 comment

#74 - implement BLINK method in rMVP

Issue - State: open - Opened by binlu1981 over 2 years ago

#73 - set encoded sex as factor or numeric

Issue - State: open - Opened by binlu1981 over 2 years ago - 1 comment

#72 - identical result from GLM and FarmCPU

Issue - State: open - Opened by binlu1981 over 2 years ago - 5 comments

#71 - error in MVP.Data.Numeric2MVP processing separator

Issue - State: open - Opened by liusy-jz over 2 years ago

#70 - Can combine multiple covariates and load as single covariates file

Issue - State: open - Opened by shameem356 over 2 years ago - 4 comments

#69 - Can I directly use the imputation data (in vcf format) from Michigan Impuation server or TOPMed Imputation server without the need to modify data?

Issue - State: open - Opened by ashaked about 3 years ago

#68 - Can't install rmVP

Issue - State: closed - Opened by TinaNeik339 about 3 years ago - 3 comments

#67 - issure about PC

Issue - State: open - Opened by Feng560 about 3 years ago - 4 comments

#66 - Genome-wide threshold input

Issue - State: closed - Opened by zokozen about 3 years ago

#65 - Lots of snp sites with extreamly high P value

Issue - State: open - Opened by Dkyuan about 3 years ago - 4 comments

#64 - MVP pvalue permutation returned

Issue - State: closed - Opened by jrod55 over 3 years ago - 2 comments

#63 - Error loading hapmap and vcf files

Issue - State: open - Opened by PaulineSnor over 3 years ago - 4 comments

#62 - If i have genotype data in Numeric format, do I need to adjust the order of genotype file to be consistent with phenotype and map file?

Issue - State: open - Opened by biolittleboy over 3 years ago - 1 comment

#61 - Error: Could not find tools necessary to compile a package

Issue - State: closed - Opened by TinaNeik339 over 3 years ago - 1 comment
Labels: Installation error

#60 - Error in MVP.Data

Issue - State: closed - Opened by TinaNeik339 over 3 years ago - 2 comments

#59 - How to export PCA matrix?

Issue - State: closed - Opened by Arthur1021 over 3 years ago - 1 comment
Labels: question

#58 - How to use of FDR adjusted Pvalues for threshold at 0.05 and 0.01 level of significance

Issue - State: open - Opened by sakhale2 over 3 years ago - 3 comments

#57 - Different output from GAPIT Farmcpu and rMVP Farmcpu

Issue - State: open - Opened by shameem356 over 3 years ago - 3 comments

#56 - Is it possible to apply the program to haploid dataset?

Issue - State: open - Opened by WangYue0926 over 3 years ago - 2 comments

#55 - What's the change of 1.0.3 to 1.0.4?

Issue - State: closed - Opened by Jiny000 over 3 years ago - 2 comments

#54 - Changing marker size for bonferoni correction

Issue - State: closed - Opened by mtross2 over 3 years ago - 2 comments

#53 - Feature request: Add N, Allele1 and Allele2 info to MVP output

Issue - State: open - Opened by songtaogui over 3 years ago - 1 comment
Labels: enhancement

#52 - permutation quantile

Issue - State: closed - Opened by micwij over 3 years ago - 6 comments

#51 - could not find function "MVP.Data"

Issue - State: closed - Opened by rupesht over 3 years ago - 2 comments

#50 - NA value for se in the GWAS output

Issue - State: open - Opened by Warsame2018 about 4 years ago - 1 comment

#49 - Incomplete Manhattan plots

Issue - State: closed - Opened by MuBulut about 4 years ago - 24 comments

#48 - Installation problem rMVP

Issue - State: closed - Opened by rupesht about 4 years ago - 34 comments

#47 - Error in svd(X) : infinite or missing values in 'x'

Issue - State: closed - Opened by Rudrakshi1234 over 4 years ago - 15 comments

#46 - Indels in HapMap file

Issue - State: closed - Opened by ghost over 4 years ago - 2 comments

#45 - MVP.Report all traits in separated axes

Issue - State: closed - Opened by shenweima over 4 years ago - 2 comments

#44 - Two minor bugs

Issue - State: closed - Opened by philippbayer over 4 years ago - 2 comments

#43 - Typos fixed on lines 540 & 542

Pull Request - State: closed - Opened by kant over 4 years ago

#42 - Do you plan to have Julia package?

Issue - State: closed - Opened by zhaotianjing almost 5 years ago - 2 comments

#41 - set color for SNP density figure

Issue - State: closed - Opened by shenweima almost 5 years ago - 4 comments
Labels: question

#40 - Error in big.matrix

Issue - State: closed - Opened by Wangchangsh almost 5 years ago - 4 comments

#39 - nPC.GLM, nPC.MLM and nPC.FarmCPU

Issue - State: closed - Opened by shenweima almost 5 years ago - 2 comments
Labels: question

#38 - cannot install the rMVP package

Issue - State: closed - Opened by yuluc almost 5 years ago - 9 comments
Labels: Installation error

#37 - figure in ppt format

Issue - State: open - Opened by shenweima almost 5 years ago - 1 comment
Labels: enhancement

#36 - infinite or missing values in 'x'

Issue - State: closed - Opened by liubei8852 about 5 years ago - 2 comments
Labels: question

#35 - error while installing [email protected] in R version 3.6.0

Issue - State: closed - Opened by avinashkarn about 5 years ago - 2 comments
Labels: Installation error

#34 - Error in svd(x, nu = 0, nv = k) : infinite or missing values in 'x'

Issue - State: closed - Opened by philippbayer over 5 years ago - 18 comments

#33 - Submit to Bioconductor / release 0.99.15

Issue - State: closed - Opened by hyacz over 5 years ago
Labels: enhancement

#32 - multiple trait analysis issues

Issue - State: closed - Opened by Arthur1021 over 5 years ago - 2 comments
Labels: bad configuration

#31 - mvp.pc.txt and mvp.kin.txt

Issue - State: closed - Opened by liqingbioinfo over 5 years ago - 2 comments

#30 - Unusual FarmCPU results

Issue - State: closed - Opened by strei102 over 5 years ago - 2 comments
Labels: question

#29 - Issue with loading vcf file

Issue - State: closed - Opened by strei102 over 5 years ago - 4 comments

#28 - Problem to read Numeric data

Issue - State: closed - Opened by TinaNeik over 5 years ago - 42 comments
Labels: input error

#27 - Matrix dimensions do not agree

Issue - State: closed - Opened by vbern almost 6 years ago - 2 comments
Labels: enhancement, bad configuration

#26 - PVE value

Issue - State: closed - Opened by huangl07 almost 6 years ago - 2 comments
Labels: enhancement, question

#25 - Multi-Trait Manhattan Plot Issues

Issue - State: closed - Opened by jhurst5 almost 6 years ago - 2 comments
Labels: enhancement, question

#24 - Error in density.default(phe[, i]) : 'x' contains missing values

Issue - State: closed - Opened by jhurst5 almost 6 years ago - 4 comments
Labels: Installation error

#23 - output permutation threshold

Issue - State: closed - Opened by mdellh2o about 6 years ago - 2 comments
Labels: question

#22 - When calculating kinship, "Error: cannot allocate vector of size 56.4 Gb"

Issue - State: closed - Opened by naglemi about 6 years ago - 4 comments
Labels: bad configuration

#21 - Missing genotype, PC, kinship data in MVP.Data output from .vcf

Issue - State: closed - Opened by naglemi about 6 years ago - 9 comments
Labels: input error

#20 - Error in big.PCA

Issue - State: closed - Opened by TinaNeik about 6 years ago - 6 comments
Labels: Installation error

#19 - cite MVP

Issue - State: closed - Opened by qgao2 over 6 years ago - 5 comments
Labels: question

#18 - Windows在安装最后一步时总是不成功怎么办

Issue - State: closed - Opened by xi532654980 over 6 years ago - 2 comments
Labels: question, Installation error

#17 - What method does MVP use to calculate PC?

Issue - State: closed - Opened by jhurst5 over 6 years ago - 1 comment
Labels: question

#16 - Error in if (Max <= 1) { : missing value where TRUE/FALSE needed Calls: MVP.Report Execution halted

Issue - State: closed - Opened by alessandrotestori over 6 years ago - 2 comments

#15 - installation error - rfunction

Issue - State: closed - Opened by Charlestehn over 6 years ago - 2 comments
Labels: Installation error

#14 - use significant SNP as CV, permutation of FarmCPU

Issue - State: closed - Opened by tanyongjun0815 over 6 years ago - 3 comments
Labels: question

#13 - Error in solve.default(ww)

Issue - State: closed - Opened by Chase556677 over 6 years ago - 2 comments
Labels: bad configuration

#12 - Error: $ operator is invalid for atomic vectors

Issue - State: closed - Opened by jhurst5 over 6 years ago - 5 comments

#11 - Error in running MVP: Error in SetAll.bm(x, value)

Issue - State: closed - Opened by qgao2 over 6 years ago - 22 comments
Labels: input error

#10 - unexpected numeric constant

Issue - State: closed - Opened by jhurst5 over 6 years ago - 7 comments

#9 - best way to convert SNP genotype to numeric matrix

Issue - State: closed - Opened by qgao2 over 6 years ago - 4 comments
Labels: enhancement

#8 - multi phenotype

Issue - State: closed - Opened by huangl12138 over 6 years ago - 4 comments
Labels: question

#7 - Error in install.packages(pkg, repos = NULL) : type == "both" cannot be used with 'repos = NULL'

Issue - State: closed - Opened by angelaparodymerino over 6 years ago - 3 comments
Labels: Installation error

#6 - Eigen::internal::tridiagonal_qr_step rfunctions install error!

Issue - State: closed - Opened by huangl12138 over 6 years ago - 5 comments
Labels: Installation error

#5 - Error in seq.default(0, maxbin.num, len) : invalid '(to - from)/by'

Issue - State: closed - Opened by avinashkarn over 6 years ago - 3 comments
Labels: Installation error

#4 - NA phenotype

Issue - State: closed - Opened by ghost almost 7 years ago - 8 comments
Labels: bug

#3 - Adjusted some format

Pull Request - State: closed - Opened by hyacz almost 7 years ago

#2 - README.md

Pull Request - State: closed - Opened by YinLiLin about 7 years ago

#1 - YinLL Update README.md

Pull Request - State: closed - Opened by YinLiLin about 7 years ago

GitHub / xiaolei-lab/rMVP issues and pull requests