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readvcf
•
reset
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
9.0 years ago
pifferdavide
• 0
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.1 years ago • updated 9.0 years ago
dan.gatti
• 0
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.1 years ago by
naive
• 0
1
vote
12
replies
2.8k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
Kipper Fletez-Brant
▴ 150
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
9.0 years ago
askates
▴ 10
0
votes
4
replies
2.7k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
8.4 years ago
Marcin Grzybowski
• 0
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.8 years ago
Didi
▴ 10
2
votes
3
replies
2.2k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.2 years ago
summerela
• 0
0
votes
2
replies
2.1k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
9.1 years ago
mjsduncan
• 0
1
vote
4
replies
2.1k
views
cannot allocate memory?
readVcf
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Haiying.Kong
▴ 110
2
votes
4
replies
1.9k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
ruben.drews
• 0
3
votes
4
replies
1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 5.8 years ago by
Michael Lawrence
★ 11k • written 5.8 years ago by
david.mas
• 0
0
votes
5
replies
1.7k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
JK
▴ 10
0
votes
2
replies
1.6k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 7.9 years ago by
Michael Lawrence
★ 11k • written 7.9 years ago by
emily.mccann
• 0
0
votes
2
replies
1.6k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
nicolas.o.rode
• 0
0
votes
1
reply
1.5k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.2 years ago by
Julian Gehring
★ 1.3k • written 8.2 years ago by
jolligoodfellow
• 0
0
votes
1
reply
1.5k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
9.4 years ago
jls2282
• 0
2
votes
1
reply
1.4k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
Simon Coetzee
▴ 50
2
votes
3
replies
1.3k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Peter Hickey
▴ 740
0
votes
2
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.1 years ago
naive
• 0
1
vote
1
reply
1.1k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
fongchunchan
▴ 30
0
votes
2
replies
1.0k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
7.2 years ago
TimothéeFlutre
▴ 80
0
votes
0
replies
484
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
14 months ago
therealgenna
• 0
23 results • Page
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Replies
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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