Thank you for updating to provide the bootstrap probability for each gene. However, I met an error that was not seen in 1.6.0 when I performed EWCE::bootstrap_enrichment_test()
# Paste console output here (e.g. from R/python/command line)
> full_results <- EWCE::bootstrap_enrichment_test(sct_data = our_ctd_data_human,
+ sctSpecies = "human",
+ genelistSpecies = "human",
+ output_species = "human",
+ method = "homologene",
+ hits = hits,
+ reps = 100,
+ annotLevel = 1)
1 core(s) assigned as workers (7 reserved).
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Standardising CellTypeDataset
+ <2 non-zero quantile bins detected in column. Assigning these values to default quantile ( 20 )
Checking gene list inputs.
Returning 19,129 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
733 hit genes remain after filtering.
Computing gene scores.
Using previously sampled genes.
Error in exp_mats[[cc]][s, ] <- sort(expD[, cc]) :
replacement has length zero
### Expected behaviour
(A clear and concise description of what you expected to happen.)
There was no error in 1.6.0 version
## 2. Reproducible example
### Code
our_ctd = EWCE::generate_celltype_data(exp=human_spine_rds@assays$RNA@counts,annotLevels=list(cellType=human_spine_rds$cell_type2),groupName="human_RDS")
our_ctd_data_human = load_rdata(our_ctd)
risk_genes = read.table(genetic_path)
hits = as.vector(unlist(risk_genes))
print(hits)
reps <- 1500
annotLevel <- 1
full_results <- EWCE::bootstrap_enrichment_test(sct_data = our_ctd_data_human,
sctSpecies = "human",
genelistSpecies = "human",
output_species = "human",
method = "homologene",
hits = hits,
reps = 100,
annotLevel = 1)
```R
# Paste example here
1. Bug description
Thank you for updating to provide the bootstrap probability for each gene. However, I met an error that was not seen in 1.6.0 when I performed EWCE::bootstrap_enrichment_test()
Console output
Data
This is how my ctd data looks like:
3. Session info
(Add output of the R function
utils::sessionInfo()below. This helps us assess version/OS conflicts which could be causing bugs.)Details