Commit 86028f90 authored by mirachirkova's avatar mirachirkova
Browse files

fix readme

parent d7a3080e
......@@ -122,137 +122,65 @@ Source files description
-----------------
- **install.R** \
\
Installs all required R packages.
Installs all required R packages.\
**Example**:
>Rscript install.R
`Rscript install.R`
- **run.R** \
Contains all the pipeline. It needs three command arguments - count
matrix file name, table annotation file name and output directory name.
See output of run.R in output data paragraph of readme.
See output of run.R in output data paragraph of readme.\
Imports functions from **source/DESeq.R**, **source/EBSeq.R**,
**source/edgeR.R**, **source/NOISeq.R**, **source/voom.R**,
**source/signatures_utils.R**, **source/calculate_distmatrix_utils.R**
**source/signatures_utils.R**, **source/calculate_distmatrix_utils.R** \
**Example**: \
`Rscript run.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput`
**Example**:
>Rscript run.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput
- **source/pipeline_parts/de_analysis.R**\
Computes differential expression for all tools. Returns **'\*_res.rds'**
files and **'\*_plot.pdf'** files. Imports functions from **source/DESeq.R**,
**source/EBSeq.R**, **source/edgeR.R**, **source/NOISeq.R**,
**source/voom.R**. It needs three command arguments - count
matrix file name, table annotation file name and output directory name.
matrix file name, table annotation file name and output directory name. \
**Example**:
>Rscript source/pipeline_parts/de_analysis.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput
`Rscript source/pipeline_parts/de_analysis.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput`
- **source/pipeline_parts/signatures_making.R**\
Makes **'\*_sig.txt'** files using **'\*_res.rds'** files and chosen
signature. Imports functions from **source/signatures_utils.R**.
It needs three command arguments - count matrix file name, table
annotation file name and output directory name.
annotation file name and output directory name. \
**Example**: \
`Rscript source/pipeline_parts/signatures_making.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput`
**Example**:
>Rscript source/pipeline_parts/signatures_making.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput
- **source/pipeline_parts/calculate_distmatrix.R**\
Makes **'\*_sig.txt.distmatrix'** files using **'\*_sig.txt'** files.
Imports functions from **source/calculate_distmatrix_utils.R**
It needs three command arguments - count matrix file name, table
annotation file name and output directory name.
**Example**:
> Rscript source/pipeline_parts/calculate_distmatrix.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput
annotation file name and output directory name.\
**Example**: \
`Rscript source/pipeline_parts/calculate_distmatrix.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput`
- **source/pipeline_parts/calculate_hobotnica.R**\
Makes **'hobotnica_scores.txt'** file using **'\*_sig.txt.distmatrix'**
files.
Imports functions from **hobotnica/R/Hobotnica.R**
It needs three command arguments - count matrix file name, table
annotation file name and output directory name.
annotation file name and output directory name.
**Example**:
> Rscript source/pipeline_parts/calculate_distmatrix.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput
- **source/DESeq.R**, **source/EBSeq.R**, **source/edgeR.R**,
**source/NOISeq.R**, **source/voom.R**\
\
Contain functions related to a specific tool. \
\
***\*\_f(counts, coldata)*** - computes differential expression, where *count*
is matrix of count and *coldata* is prepared for usage information about
conditions.\
\
***\*\_v(\*\_res, out)*** - visualizes differential expression. *\*\_res* - is a
result of differential expression analysis. *out* is name for
output directory\
\
***\*\_top(results, n)*** - makes subset of top-n expressed genes. *results*
is a result of differential expression analysis, *n* - is a number
of genes in top.\
\
***\*\_filtered(results)*** - makes subset of filtered genes. *results* - is a
result of differential expression analysis. *Have a strange results, better
not to use.*
- **source/signatures_utils.R**\
\
Contains functions for subset making.\
\
***top_signature(results_deseq2, results_ebseq, results_edger, results_voom,
results_noiseq, n, out)*** - makes **'\*_sig.txt'** files using top-n signature.
Arguments are results of differential expression analysis and *n* -
number of genes in top. *out* is name for
output directory\
\
***filtered_signature(results_deseq2, results_ebseq, results_edger,
results_voom, results_noiseq, out)*** - makes **'\*_sig.txt'** files using
filtering. Arguments are results of differential expression analysis. *Have
a strange results, better not to use.* *out* is name for
output directory\
\
***draw_venn_diag(out)*** - plots Venn diagram. Uses as constant that names:
**'DESeq_sig.txt.distmatrix'**, **'EBSeq_sig.txt.distmatrix'**,
**'edgeR_sig.txt.distmatrix'**, **'NOISeq_sig.txt.distmatrix'** and
**'voom_sig.txt.distmatrix'**. If one of the subset does not exist,
skip it. *out* is name for
output directory
- **source/calculate_distmatrix_utils.R** \
\
Contains functions for distance matrix making.\
\
***calculate_distmatrix(countMatrixFile, signatureFile)*** - makes
**'\*_sig.txt.distmatrix'** from count matrix *countMatrixFile* and
subset *signatureFile*.\
- **source/hobotnica_using.R**\
\
Contains functions for using Hobotnica tool.\
\
***calculate_hobotnica (distmat, condition)*** - calculate
Hobotnica score for certain distance matrix *distmat* and
list of conditions for each sample *condition*.\
\
***use_hobotnica (deseq_distmat, ebseq_distmat, \
edger_distmat, voom_distmat, noiseq_distmat, \
condition, out)*** - calculate Hobotnica score for all tool's
distance matrixes, which are first 5 arguments
and list of conditions for each sample *condition*. *out* is name for
output directory
`Rscript source/pipeline_parts/calculate_distmatrix.R data/TCGA_prostate_countmatrix.txt
data/annotation_TCGA_prostate.txt ouput`
Other files were not made for executing and contain functions for different parts of the pipelines.
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