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Al-Murphy
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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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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
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