xiaojieqiu / github_test

This repository is used to test all github operations

github_test

This repository is used to test all github operations

github_test's Issues

(monocle)Why I can't find a ID column in my data and cds fvarLabels.?plot_genes_in_pseudotime functions relies on this column, but I can't find "id" .

@Xiaojieqiu Why I can't find a ID column in my data and cds fvarLabels.?plot_genes_in_pseudotime functions relies on this column, but I can't find "id" .

> my_pseudotime_de %>% arrange(qval) %>% head()
  status           family pval qval gene_short_name num_cells_expressed use_for_ordering
1     OK negbinomial.size    0    0        Serpine2                2330             TRUE
2     OK negbinomial.size    0    0           Ramp1                1623             TRUE
3     OK negbinomial.size    0    0             Dbi                5190             TRUE
4     OK negbinomial.size    0    0          Pea15a                3707             TRUE
5     OK negbinomial.size    0    0          Atp1a2                1789             TRUE
6     OK negbinomial.size    0    0            Gatm                1587             TRUE
> tdcds
CellDataSet (storageMode: environment)
assayData: 54233 features, 5621 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: AAACCTGAGCAGCGTA AAACGGGCAGCTCGCA ... TGCTACCGTCGGCACT (5621 total)
  varLabels: orig.ident nCount_RNA ... State (15 total)
  varMetadata: labelDescription
featureData
  featureNames: 4933401J01Rik Gm26206 ... tdTomato (54233 total)
  fvarLabels: gene_short_name num_cells_expressed use_for_ordering
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

I follow this turtorial to do monocle analysis,in his picture,he selected the top 6 genes using "id", and there is a" id "among fvarLabels in his featureData,like this:


Can you help me?