devel_notes.md 1.81 KB
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Links & Todo
------------


[Best Way To Quantify Influence Of Different Covariates On Gene Expression?](https://www.biostars.org/p/97624/)


Other enrichment tools
* http://amp.pharm.mssm.edu/Enrichr/
* http://amp.pharm.mssm.edu/Harmonizome/
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* [piano](http://www.bioconductor.org/packages/release/bioc/html/piano.html)
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IHW Eval
--------

```
> results(dds, contrast = c(contrastAttribute, sample_1, sample_2)) %>%
+     tibble::as_data_frame("foo") %>%
+     count(padj < 0.01)
# A tibble: 3 × 2
  `padj < 0.01`     n
          <lgl> <int>
1         FALSE 12573
2          TRUE  9151
3            NA  2349
Warning message:
In as.data.frame(x, row.names = NULL, optional = optional, ...) :
  Arguments in '...' ignored
> 
> results(dds, contrast = c(contrastAttribute, sample_1, sample_2), lfcThreshold = lfc_cutoff) %>%
+     tbl_df %>%
+     count(padj < 0.01)
# A tibble: 3 × 2
  `padj < 0.01`     n
          <lgl> <int>
1         FALSE 17789
2          TRUE  3002
3            NA  3282
Warning message:
In as.data.frame(x, row.names = NULL, optional = optional, ...) :
  Arguments in '...' ignored
> 
> ihwResults = results(dds, contrast = c(contrastAttribute, sample_1, sample_2), lfcThreshold = lfc_cutoff, filterFun = ihw) %>%
+     tbl_df %>%
+     tibble::rownames_to_column("ensembl_gene_id")
Warning message:
In as.data.frame(x, row.names = NULL, optional = optional, ...) :
  Arguments in '...' ignored
> 
> ihwResults %>% count(padj < 0.01)
# A tibble: 3 × 2
  `padj < 0.01`     n
          <lgl> <int>
1         FALSE 21021
2          TRUE  3037
3            NA    15
> 

```
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How to report used version for a project?
-----------------------------------------

```bash
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(cd ${NGS_TOOLS} && test -n "${PRJ_NAME}" && git diff --exit-code && git rev-parse HEAD  >> ${PRJ_DATA}/.used_ngs_tools )  || echo "pending changes in ngs_tools"
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```