Comments (1)
Read the OUTRIDER dataset object (ods). It is located under /processed_results/aberrant_expression/{genomeAssembly}/outrider/{DROP_GROUP}/ods.Rds
Run the plotCountCorHeatmap function, for example:
ods <- OUTRIDER::plotCountCorHeatmap(ods, nRowCluster = 4, nColCluster = 3, normalized = FALSE)
normalized = FALSE -> obtain the clustering of the samples before correction
nRowCluster and nColCluster define the number of clusters to assign samples to
By assigning the command to the ods, it adds 2 columns to the colData part of the object (describing the samples) with the cluster number where each sample was assigned to for the clustering with 4 groups and 3 groups.
You can access those columns by doing:
colData(ods)$clusterNumber_4
colData(ods)$clusterNumber_3
For more details, please refer to the OUTRIDER documentation, section 4.3 http://bioconductor.org/packages/release/bioc/vignettes/OUTRIDER/inst/doc/OUTRIDER.pdf
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Related Issues (20)
- Error in merge.data.table() - AberrantExpression_pipeline_OUTRIDER_pvalsOutrider_R HOT 3
- no suitable codecs found HOT 1
- Estimated run-time for FRASER2 HOT 13
- drop demo fails at rnaVariantCalling/pipeline/Snakefile line 446 HOT 18
- Error in rule MonoallelicExpression_pipeline_QC_create_matrix_dna_rna_cor_R: HOT 4
- Error in rule changeHeader HOT 7
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: HOT 10
- No paired-end reads were detected in paired-end read library HOT 9
- Error in FRASER_Summary_R HOT 4
- Error in rule AberrantSplicing_pipeline_FRASER_Summary_R: HOT 3
- Error in bamFile(fds[, samples(fds) == sampleID])[[1]] HOT 1
- Error in AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R HOT 29
- Using external count in FRASER2? HOT 5
- Is it possible to use drop without snakemake? HOT 1
- DROP_1.3.3.yaml package update required? HOT 7
- drop demo not working: Error in find_NCBI_assembly_ftp_dir HOT 4
- Missed call - not clear why HOT 2
- Error in rule AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R HOT 3
- Error in reducer$value.cache[[as.character(idx)]] <- values HOT 8
- MissingInputException: Missing input files for rule mae_allelicCounts: HOT 7
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