Commit 2cf2a8df authored by Olesya's avatar Olesya 🐋
Browse files

Merge branch 'master' into dev

parents c95a334d 9423fe4b
......@@ -12,7 +12,7 @@ General usage notes
between two experimental conditions by 5 tools: DESeq, EBSeq, edgeR,
limma voom and NOISeq.
- Program also computes distance matrixes using different types of signatures,
that can be used in Hobotnica to compare results and calculate the best
and uses it in Hobotnica to compare results and calculate the best
differential expression tool for input data. It also visualizes intersection
of subsets.
......@@ -65,6 +65,9 @@ names are **'DESeq_sig.txt'**, **'EBSeq_sig.txt'**, **'edgeR_sig.txt'**,
Program also plots Venn diagram that shows intersection of different tools
subsets. File name is **'venn_diagram.pdf'**.
File **'hobotnica_scores.txt'** contains results of Hobotnica computing
for each tool.
---------------------------------------------------------------------------
Quick start
......@@ -201,10 +204,26 @@ Contains functions for distance matrix making.
**'\*_sig.txt.distmatrix'** from count matrix *countMatrixFile* and
subset *signatureFile*.
*calculate_distmatrixes (countMatrixFile)* - makes all
***calculate_distmatrixes (countMatrixFile)*** - makes all
**'\*_sig.txt.distmatrix'** files from from count matrix
***countMatrixFile***. Uses as constant that names:
**'DESeq_sig.txt.distmatrix'**, **'EBSeq_sig.txt.distmatrix'** ,
*countMatrixFile*. Uses that file names to download data about subsets:
**'DESeq_sig.txt'**, **'EBSeq_sig.txt'** ,
**'edgeR_sig.txt'**, **'NOISeq_sig.txt'** and
**'voom_sig.txt'**.
- **source/hobotnica_using.R**
Contains functions for using Hobotnica tool.
***calculate_hobotnica (distmat_filename, condition)*** - calculate
Hobotnica score for certain distance matrix *distmat_filename* and
list of conditions for each sample *condition*.
***use_hobotnica (condition)*** - calculate
Hobotnica score for all tool's distance matrixes and
list of conditions for each sample *condition*. Uses that file names
to download data about: **'DESeq_sig.txt.distmatrix'**,
**'EBSeq_sig.txt.distmatrix'** ,
**'edgeR_sig.txt.distmatrix'**, **'NOISeq_sig.txt.distmatrix'** and
**'voom_sig.txt.distmatrix'**.
......@@ -215,7 +234,7 @@ Current problems
- A lot of unuseful information in output.
- ***filtered_signature*** signature is unrepresentative. Perhaps every
tool has their own sensitiveness for logFC, p-value etc.
- Need to insert Hobotnica scoring functions and part of the pipeline description
- Download some other features.
......
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