Comments (5)
You can use the labelKeep function… see vignette.
from fishpond.
Hi,
I noted that, and I have run
y <- labelKeep(y)
y <- y[mcols(y)$keep,]
from fishpond.
My full code is:
y <- importAllelicCounts(
sample_tximeta, a1="L", a2="R",
format="wide", tx2gene=tx2gene.1
)
y <- labelKeep(y)
y <- y[mcols(y)$keep,]
y <- fishpond::swish(y, x="allele", pair="samples",
cov="time", cor="pearson")
from fishpond.
Oh right. I forgot the right code to use.
See this code chunk
https://thelovelab.github.io/fishpond/articles/allelic.html#filtering-features
from fishpond.
Hi,
Its work well, thank you for your help
Regrads,
Zhang
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Related Issues (16)
- support of sparsed Matrix output of alevin HOT 6
- Error in dbFileConnect(file) HOT 2
- Error in infRepError(infRepIdx) : there are no inferential replicates in the assays of 'y' HOT 1
- matrixStats::rowRanks(): Specify argument 'ties.method = "max"' to avoid being affected by future updates HOT 3
- One-sample t-test for paired design HOT 1
- plotInfReps y axis mislabel HOT 2
- Allelic plots should offer to customize allelic labels
- Using loadFry for HTO quantifications HOT 5
- Extend to ordinal conditions HOT 7
- R CMD check WARNING: Requires (indirectly) orphaned package: ‘gtools’ HOT 3
- How to output the scaled counts for each sample HOT 3
- gene_ids after summarising counts with loadFry HOT 5
- Add definition of InfRV to computeInfRV
- Wrong index in randomSamplesToRemove() HOT 4
- Unused argument (diffAI = TRUE) HOT 5
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