Al-Murphy MungeSumstats issues

Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

https://doi.org/doi:10.18129/B9.bioc.MungeSumstats

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issues

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Allow user-defined `sumstatsColHeaders` mapping as argument

#45 albert-ying closed 3 years ago
2
When `allele_filp_check = TRUE` , allele frequence should also be filped

#44 albert-ying closed 3 years ago
4
Compute effective sample size

#43 bschilder closed 3 years ago
1
BiocCheck: WARNING: Add non-empty \value sections to the following man pages:

#42 bschilder closed 3 years ago
1
BiocCheck: ERROR: Avoid references to external hosting platforms

#41 bschilder closed 3 years ago
0
Warning in readLines(infile) : incomplete final line found

#40 bschilder closed 3 years ago
2
BiocCheck :* ERROR: Packages providing 2 object(s) used in this package should be imported in the NAMESPACE file

#39 bschilder closed 3 years ago
3
Change tests to be more robust

#38 bschilder closed 3 years ago
0
Standardise chromosome format

#37 bschilder closed 3 years ago
2
`test_that("non-biallelic SNPs are removed",` failing

#36 bschilder closed 3 years ago
2
Add note about MungeSumstats being for human-only data

#35 bschilder closed 3 years ago
0
Account for sitations where there's a mismatch between write_vcf and save_path

#34 bschilder closed 3 years ago
0
Saved formatted files disappear after restarting R session

#33 bschilder closed 3 years ago
5
Report how many SNPs you started with.

#32 bschilder closed 3 years ago
0
Ensure all X and Y chromosomes are uppercase

#31 bschilder closed 3 years ago
1
Use formatC for more readable reports

#30 bschilder closed 3 years ago
2
Add N_dropNA arg

#29 bschilder closed 3 years ago
0
Error in ids2rowids(ids) : 'ids' cannot contain NAs

#28 bschilder closed 3 years ago
2
Speed up VCF download

#27 bschilder closed 3 years ago
1
non-numeric argument to mathematical function

#26 bschilder closed 3 years ago
1
Add metadata to saved VCFs

#25 bschilder opened 3 years ago
0
Recognize previously formatted files of the same name

#24 bschilder closed 3 years ago
0
Error in ids2rowids(ids) :

#23 bschilder closed 3 years ago
6
Create search function to find datasets of interest on Open GWAS

#22 bschilder closed 3 years ago
3
Add alternative means of getting sample ID from VCF

#21 bschilder closed 3 years ago
0
read VCF with data.table

#20 bschilder closed 3 years ago
0
Return sum stats as GRanges or VRanges

#19 bschilder closed 3 years ago
1
Option to write as VCF

#18 bschilder closed 3 years ago
7
Allow users to return data directly

#17 bschilder closed 3 years ago
0
Add header hashes for quick reference in Rstudio

#16 bschilder closed 3 years ago
0
Read data with`data.table::fread()`

#15 bschilder closed 3 years ago
1
Make `data.table::copy()` explicit

#14 bschilder closed 3 years ago
0
Make arguments explicit

#13 bschilder closed 3 years ago
0
`sumstatsColHeaders` variable missing

#12 bschilder closed 3 years ago
9
Allow users to supply the file in-memory

#11 bschilder closed 3 years ago
1
Allow users to specify output path

#10 bschilder closed 3 years ago
0
Provide API-access to MRC IEU Open GWAS

#9 bschilder closed 3 years ago
1
Sort sum stats by genomic coordinates

#8 bschilder closed 3 years ago
2
Option to tabix-index

#7 bschilder closed 3 years ago
2
Speed improvements

#6 bschilder closed 3 years ago
3
Account for INFO with all NAs

#5 bschilder closed 3 years ago
1
Add progress indicators / improve messages

#4 bschilder closed 3 years ago
2
Output results as *.gz for LDSC ready format

#3 Al-Murphy closed 3 years ago
7
Add function to infer MAF

#2 Al-Murphy closed 3 years ago
1
is the vignette properly formatted

#1 vjcitn closed 3 years ago
1