Commit 6c513ba9 authored by Holger Brandl's avatar Holger Brandl

updated docs and dependencies

parent 5390f814
File mode changed from 100644 to 100755
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
---------------------------
......
File mode changed from 100644 to 100755
File mode changed from 100644 to 100755
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