rqtl/qtl2 issues and pull requests

#235 - Extreme values from scan1coef

Issue - State: closed - Opened by kieranatkins 3 months ago - 2 comments

#234 - use multiple cores in scan1_pg.R routine scan1_pg_clean

Pull Request - State: closed - Opened by byandell 3 months ago - 1 comment

#233 - New version on CRAN: 0.36

Pull Request - State: closed - Opened by kbroman 4 months ago

#232 - SDP panel not working in plot_snpinfo() plots?

Issue - State: closed - Opened by kbroman 6 months ago - 1 comment
Labels: bug

#231 - Fix compiler warning on CRAN

Pull Request - State: closed - Opened by kbroman 10 months ago

#230 - Compiler warning on CRAN

Issue - State: closed - Opened by kbroman 10 months ago

#229 - Implement find_dup_markers(), port of qtl::findDupMarkers()

Pull Request - State: closed - Opened by kbroman 11 months ago

#228 - possible bug in chisq_colpairs()

Issue - State: closed - Opened by kbroman 11 months ago
Labels: bug

#227 - remove intcovar mention in scan1blup help

Issue - State: closed - Opened by kbroman 11 months ago
Labels: documentation

#226 - Genotype format conversion for multiparental MAGIC populations 123

Issue - State: closed - Opened by jamonterotena 11 months ago - 1 comment

#225 - Implement findDupMarkers()

Issue - State: closed - Opened by kbroman 12 months ago
Labels: enhancement

#224 - Effects of using pmap instead of gmap

Issue - State: closed - Opened by micwij about 1 year ago - 3 comments

#223 - qtl2::read_csv() masks readr::read_csv()

Issue - State: closed - Opened by micwij about 1 year ago - 2 comments

#222 - Link to function man pages

Issue - State: closed - Opened by kbroman about 1 year ago - 1 comment
Labels: documentation

#221 - Add explanation of weights in est_herit

Issue - State: closed - Opened by gtsambos about 1 year ago - 3 comments

#220 - calc_het() assumes 2-char genotypes

Issue - State: closed - Opened by kbroman about 1 year ago
Labels: bug

#219 - scan1snps(): subset genoprobs and map to same positions

Issue - State: closed - Opened by kbroman over 1 year ago
Labels: enhancement

#218 - Check for missing values in map in scan1snps()

Issue - State: closed - Opened by kbroman over 1 year ago
Labels: bug

#217 - changes for CRAN ver 0.32

Pull Request - State: closed - Opened by kbroman over 1 year ago

#216 - plot_genes() allow strand to be numeric +/- 1rather than just char +/-

Issue - State: closed - Opened by kbroman over 1 year ago
Labels: bug

#215 - plot_snpasso() needs snp name to be "snp_id"

Issue - State: closed - Opened by kbroman over 1 year ago - 2 comments
Labels: bug

#214 - Give warning if sex isn't provided but is needed

Issue - State: closed - Opened by kbroman over 1 year ago

#213 - yaml and genotype file format

Issue - State: closed - Opened by yifangt almost 2 years ago - 1 comment

#212 - Corrections for DOF1/HSF1 data

Pull Request - State: closed - Opened by kbroman almost 2 years ago - 1 comment

#211 - Give warning if cross contains unneeded founder_geno

Issue - State: closed - Opened by kbroman almost 2 years ago
Labels: enhancement

#210 - Seems like predict_snpgeno don't work for DOF1 data

Issue - State: closed - Opened by kbroman almost 2 years ago - 2 comments
Labels: bug

#209 - Odd warning in read_cross2

Issue - State: closed - Opened by kbroman almost 2 years ago
Labels: bug

#208 - Can I generate a genetic map with R/qtl2?

Issue - State: closed - Opened by Jiseon623 about 2 years ago - 2 comments

#207 - Add warning to scan2snps if SDP missing

Issue - State: closed - Opened by kbroman about 2 years ago
Labels: enhancement

#206 - Can I use already existed probability data into qtl2

Issue - State: closed - Opened by BoraKim2018 over 2 years ago - 1 comment

#205 - convert vcf file of an haploid to run r/qtl or r/qtl2

Issue - State: closed - Opened by jeancarlier34 almost 3 years ago - 1 comment

#204 - qtl2 crashing R sessions via Rcpp

Issue - State: closed - Opened by rkmeade almost 3 years ago - 1 comment

#203 - Disregard

Issue - State: closed - Opened by SmithLabDuke almost 3 years ago

#202 - Add tutorial about switching to GRCm39

Issue - State: closed - Opened by kbroman almost 3 years ago - 1 comment
Labels: documentation

#201 - test of arrange_genes has messed up text

Issue - State: closed - Opened by kbroman almost 3 years ago

#200 - Create 4-way cross type

Issue - State: open - Opened by kbroman about 3 years ago
Labels: enhancement

#199 - In User Guide, show effect plot at QTL

Issue - State: open - Opened by kbroman about 3 years ago
Labels: documentation

#198 - Add sdp_panel arg to plot_snpasso() to show panel SNP SDPs

Pull Request - State: closed - Opened by kbroman about 3 years ago

#197 - A whole bunch of changes, including revised CC colors

Pull Request - State: closed - Opened by kbroman about 3 years ago

#196 - step() returning NaN for "genail8"

Issue - State: closed - Opened by kbroman about 3 years ago - 2 comments
Labels: bug

#195 - Bug in scan1snps() if snpinfo is incomplete

Issue - State: closed - Opened by kbroman over 3 years ago - 1 comment
Labels: bug

#194 - problem with calc_genoprob if no genetic map

Issue - State: closed - Opened by kbroman over 3 years ago
Labels: bug

#193 - SE of estimated heritability

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

#192 - zip_datafiles() not working on windows

Issue - State: open - Opened by kbroman over 3 years ago - 1 comment
Labels: bug

#191 - Create replace_ids.matrix() for replacing IDs in a matrix

Issue - State: closed - Opened by kbroman over 3 years ago
Labels: enhancement

#190 - Have calc_het() give an error if input are allele dosages

Issue - State: closed - Opened by kbroman almost 4 years ago
Labels: enhancement

#189 - ind_ids() for genoprobs object

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment
Labels: enhancement

#188 - Several small changes

Pull Request - State: closed - Opened by kbroman almost 4 years ago

#187 - Fix Issue #146 so predict_snpgeno() works with RIL

Pull Request - State: closed - Opened by kbroman almost 4 years ago

#186 - Fix a bunch of small problems

Pull Request - State: closed - Opened by kbroman almost 4 years ago

#185 - R-devel fails due to tests of plots

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment
Labels: bug

#184 - make calc_het() multi-core

Issue - State: closed - Opened by kbroman almost 4 years ago
Labels: enhancement

#183 - genoprob_to_alleleprob return NULL in riself4

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment
Labels: bug

#182 - Tutorial on detecting sample mix-ups in Diversity Outbred mice

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment
Labels: documentation

#181 - calc_het() is giving values > 1 with qtl2fst based probabilities

Issue - State: closed - Opened by kbroman almost 4 years ago
Labels: bug

#180 - If the phenotypes' rownames themselves have names...

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment
Labels: bug

#179 - Have read_cross2() give warning rather than error when possible.

Issue - State: closed - Opened by kbroman almost 4 years ago - 1 comment

#178 - Have read_cross2() give warning not error when possible

Issue - State: closed - Opened by kbroman almost 4 years ago
Labels: bug

#177 - Multi-core in scan1snps gives error about k_loco

Issue - State: open - Opened by kbroman almost 4 years ago - 3 comments
Labels: bug

#176 - guess_phase() doesn't work with cross type genail

Issue - State: closed - Opened by kbroman about 4 years ago - 2 comments
Labels: bug

#175 - Encoding of genotypes is confusing and error prone

Issue - State: open - Opened by kbroman about 4 years ago
Labels: enhancement, question

#174 - genoprob_to_alleleprob doesn't work with genail cross type

Issue - State: closed - Opened by kbroman about 4 years ago
Labels: bug

#173 - Revise reduce_markers(); fix bug in fit1()

Pull Request - State: closed - Opened by kbroman about 4 years ago

#172 - fitted values from fit1() with kinship are wrong

Issue - State: closed - Opened by kbroman about 4 years ago - 1 comment
Labels: bug

#171 - Strange read_cross2 error

Issue - State: closed - Opened by kbroman about 4 years ago - 1 comment
Labels: bug

#170 - New CRAN version fixing further problems on solaris

Pull Request - State: closed - Opened by kbroman about 4 years ago

#169 - Compiler warning about function call in brent's method

Issue - State: open - Opened by kbroman about 4 years ago - 5 comments
Labels: bug

#168 - Compiler warning about multiple enums

Issue - State: closed - Opened by kbroman about 4 years ago
Labels: bug

#167 - fixed compile error on solaris, on CRAN

Pull Request - State: closed - Opened by kbroman about 4 years ago

#166 - Small changes to get the package on CRAN

Pull Request - State: closed - Opened by kbroman about 4 years ago

#165 - Check of compatibility of map and genoprobs

Issue - State: open - Opened by kbroman about 4 years ago - 1 comment
Labels: enhancement

#164 - plot_pxg problem with y is a matrix

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: bug

#163 - Panel of SNP strain distribution patterns

Issue - State: closed - Opened by kbroman over 4 years ago - 2 comments
Labels: enhancement

#162 - Typo in documentation for scan1snps

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: documentation

#161 - speed up reduce_markers() when tons of markers

Issue - State: closed - Opened by kbroman over 4 years ago - 2 comments
Labels: enhancement

#160 - subset_ind giving odd error when IDs are like numbers

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: bug

#159 - scan1boot: bootstrap scan1()

Issue - State: open - Opened by kbroman over 4 years ago
Labels: enhancement

#158 - read_cross2 doesn't provide all warnings

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: bug

#157 - calc_genoprob should give better error re missing genetic map

Issue - State: closed - Opened by kbroman over 4 years ago
Labels: bug

#156 - Add tutorial explaining the insides of scan1snps()

Issue - State: open - Opened by kbroman over 4 years ago
Labels: documentation

#155 - genoprob_to_snpprob: snpinfo can be a cross object

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: documentation

#154 - Have fit1 return full variance matrix

Issue - State: open - Opened by kbroman over 4 years ago
Labels: enhancement

#153 - RIL self warning message on reading cross

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

#152 - fit1 should issue a warning if there are unused arguments

Issue - State: closed - Opened by kbroman over 4 years ago
Labels: bug

#151 - Allow fit1() to take no genoprobs

Issue - State: closed - Opened by kbroman over 4 years ago
Labels: enhancement

#150 - Problem with multi-core in scan1 on Windows

Issue - State: open - Opened by kbroman over 4 years ago
Labels: bug

#149 - Create an "hsf1" cross type

Issue - State: closed - Opened by kbroman over 4 years ago
Labels: enhancement

#148 - read_cross2 with multiple X chromosomes

Issue - State: closed - Opened by kbroman over 4 years ago - 1 comment
Labels: enhancement

#147 - Fix use of class()

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

#146 - predict_snpgeno() doesn't work for homozygous populations

Issue - State: closed - Opened by kbroman almost 5 years ago
Labels: bug

#145 - Fix use of class()

Issue - State: closed - Opened by kbroman almost 5 years ago

#144 - Fix use of class()

Issue - State: closed - Opened by kbroman almost 5 years ago - 1 comment

#143 - Corrections to cc_variants database

Pull Request - State: closed - Opened by kbroman almost 5 years ago

#142 - Let calc_sdp() take a vector

Issue - State: closed - Opened by kbroman almost 5 years ago
Labels: enhancement

#141 - plot_onegeno() gives a warning for DOF1 on X chromosome

Issue - State: closed - Opened by kbroman almost 5 years ago - 1 comment
Labels: bug

#140 - genoprob_to_snpprob() doesn’t work for DOF1 cross type for X chr

Issue - State: closed - Opened by kbroman almost 5 years ago - 2 comments
Labels: bug

#139 - max_scan1() gives error if no column names and lodcolumn=NULL

Issue - State: closed - Opened by kbroman almost 5 years ago
Labels: bug

#138 - Fixes to max_scan1() and maxlod()

Pull Request - State: closed - Opened by kbroman almost 5 years ago

#137 - Add lodcolumn arg for maxlod()

Issue - State: closed - Opened by kbroman almost 5 years ago
Labels: enhancement

#136 - read_csv should be more permissive about header rows

Issue - State: closed - Opened by kbroman almost 5 years ago
Labels: bug

GitHub / rqtl/qtl2 issues and pull requests