functions for meta analysis #76
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
smgogarten
reviewed
Oct 4, 2021
R/meta.R
Outdated
| BPPARAM=bpparam(), verbose=TRUE) { | ||
|
|
||
| # better way to handle these checks? | ||
| if(class(gdsobj) == 'SeqVarBlockIterator' && score.cov){ |
There was a problem hiding this comment.
should be if(is(gdsobj, "SeqVarBlockIterator") && score.cov)
Instead of having a separate score.cov logical argument, select whether to return covariance matrices by input object type. A block iterator is used for single variant tests, so only return Score and Score.SE (no covariance) for SeqVarBlockIterator objects.
…; will need separate method
smgogarten
reviewed
Oct 14, 2021
| chr=getChromosome(gdsobj, char=TRUE), | ||
| pos=getPosition(gdsobj), | ||
| stringsAsFactors=FALSE) | ||
| if (alleles) { |
There was a problem hiding this comment.
I just made a change in GWASTools so this should work now (allele columns were missing previously)
Names for group IDs in SeqVarListIterator objects may be taken from the names of the GRangesList object defining iterations. If that is NULL, it is not straightforward to construct names since variants in each group are not sequential nor even required to be on the same chromosome. Instead, number groups with sequential integers.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.