updated docs and dependencies

devel_notes.md

+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/
+
+
+
+
+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
+> 
+
+```
 
 How to tag it for a project
 ---------------------------