rqtl qtl2scan issues - Githubissues

rqtl / qtl2scan

R/qtl2 module for QTL analysis, including genome scans

http://kbroman.org/qtl2

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scan1snps gave a weird error when phenotypes were a vector

#117 kbroman closed 6 years ago
1
Add scan1snps() for single-QTL scan at SNPs

#116 kbroman closed 7 years ago
0
Improvements in interp_map()

#115 kbroman closed 7 years ago
0
Fix bug in est_herit() re linearly dependent covariates

#114 kbroman closed 7 years ago
0
Fix bug in est_herit re dependent covariate cols

#113 kbroman closed 7 years ago
0
est_herit funny behavior with missing values masking covariate

#112 byandell closed 7 years ago
2
Remove vignettes from the package

#111 kbroman closed 7 years ago
0
find_peaks_and_lod_int and find_peaks_and_bayes_int not exported in NAMESPACE

#110 dmgatti closed 7 years ago
1
Slow performance and high memory usage in qtl2scan_0.5-20

#109 dmgatti closed 6 years ago
8
Dependent cols; +/- Inf; check sizes in linreg

#108 kbroman closed 7 years ago
0
Remove preserve_intercept arg from scan1blup

#107 kbroman closed 7 years ago
0
Fix bug re decomposed kinship in scan1

#106 kbroman closed 7 years ago
0
Whole genome SNP association

#105 kbroman closed 7 years ago
4
scan1 not working if kinship matrix decomposed

#104 kbroman closed 7 years ago
0
Have est_herit return residual SD

#103 kbroman closed 6 years ago
1
Fix example contrasts for intercross

#102 kbroman closed 7 years ago
0
Align scan1 output with map in max_scan1(), find_peaks(), ...

#101 kbroman closed 7 years ago
0
In user guide, show how plot_coef can provide plot with both coefficients and the LOD curve

#100 kbroman closed 6 years ago
1
max.scan1 will give wrong results if scan1output and map don't correspond

#99 kbroman closed 7 years ago
2
scan1blup: for DO, centering BLUPs at mean makes no sense

#98 kbroman closed 7 years ago
1
effects in peak markers

#97 jcberny closed 6 years ago
2
Fix c++ code to work with RcppEigen 0.3.3.3.0

#96 kbroman closed 7 years ago
2
scan1, scan1coef, etc., for binary traits

#95 kbroman closed 7 years ago
0
decomp_kinship crashes R if ncol=nrow=0

#94 byandell closed 7 years ago
4
Bad error message from scan1 when pheno is a vector not a matrix

#93 kbroman closed 7 years ago
1
subset_scan1: use subset-by-chr approach from R/qtl2geno

#92 kbroman closed 7 years ago
0
replace 1:ncol with seq_len(ncol) to avoid problems with 0-width matr…

#91 byandell closed 7 years ago
5
Add fit1() for fitting single-QTL model at a single fixed location

#90 kbroman closed 7 years ago
0
Automatically expand number of batches in scan1perm

#89 kbroman closed 7 years ago
1
dim.calc_genoprob and dimnames.calc_genoprob for use with qtl2feather

#88 kbroman closed 7 years ago
0
replace vapply and lapply of genoprobs with dim and dimnames

#87 byandell closed 7 years ago
3
Update developer guide re removal of linemap

#86 kbroman closed 7 years ago
0
Implemented permutation test for single-QTL scan, scan1perm()

#85 kbroman closed 7 years ago
0
Major refactoring of data structures

#84 kbroman closed 7 years ago
0
interp_map: allow old and new maps to have different markers

#83 kbroman closed 7 years ago
1
Add head.scan1()

#82 kbroman closed 7 years ago
1
In scan1 and scan1blup, stop with error if cluster_lapply returns NULLs

#81 kbroman closed 7 years ago
0
Fix bug in interp_map

#80 kbroman closed 7 years ago
0
added a check for mclapply failure

#79 simecek closed 7 years ago
1
estimated QTL effects that sum to 0

#78 kbroman closed 6 years ago
1
lod in scan1 output can be missing column names

#77 kbroman closed 8 years ago
1
Drop dependent covariate columns after dropping individuals

#76 kbroman closed 7 years ago
3
When dropping NAs, also drop +/- Infs

#75 kbroman closed 7 years ago
0
Fix estimates of heritability in scan1, etc.

#74 kbroman closed 8 years ago
1
Fix error message in est_herit when total ID mismatch

#73 kbroman closed 8 years ago
1
heritability estimates off by a factor of 2?

#72 kbroman closed 8 years ago
1
Fix bug in interp_map; wasn't passing through the marker names

#71 kbroman closed 8 years ago
1
interp_map output needs to include marker names

#70 kbroman closed 8 years ago
1
User Guide: Add discussion of find_peaks, lod_int, and bayes_int

#69 kbroman closed 8 years ago
0
Fix bug in lod_int

#68 kbroman closed 8 years ago
0