Commit fe9c4b38 authored by mirachirkova's avatar mirachirkova
Browse files

fix bugs

parent 247ba4ea
......@@ -19,8 +19,7 @@ of subsets.
Input data format
-----------------
Program uses matrix of un-normalized counts, table of annotation for
each sample and name of directory for output. Optional flag is "-s",
which allows saving interim results.
each sample and name of directory for output.
The value in the i-th row and the j-th column of the count matrix tells
how many reads (or fragments, for paired-end RNA-seq) can be assigned to
......@@ -40,23 +39,25 @@ Output data
Program gives several files for each tool as output. They all are in
requested directory.
**'\*_plot.pdf'** files contain visualisation of differential expression analysis.
Expressed genes are signed. Files names are **'DESeq_plot.pdf'**,
**'EBSeq_plot.pdf'**, **'edgeR_plot.pdf'**, **'NOISeq_plot.pdf'**
and **'voom_plot.pdf'**.
**'de_plots.pdf'** file contains visualisation of differential expression analysis.
Expressed genes are signed.
**'\*_sig.txt'** files contain lists of subsets for each tool corresponding
chosen signature. Default signature is top-30 most expressed genes. Files
chosen signature. Default signature is top-30 most expressed genes. You can manually change it by set "-n" option in run.R. Files
names are **'DESeq_sig.txt'**, **'EBSeq_sig.txt'**, **'edgeR_sig.txt'**,
**'NOISeq_sig.txt'** and **'voom_sig.txt'**.
Program also plots Venn diagram that shows intersection of different tools
subsets. File name is **'venn_diagram.pdf'**.
File **'crossing.csv'** contains table with information which tool count this gene as expressed.
File **'hobotnica_scores.txt'** contains results of Hobotnica computing
for each tool.
Optionally, using "-s" flag you can save this files:
File **'crossing_with_best.csv'** contains results of the best tool and its intersection with other tools results.
Using "-s" option in run.R you can save this files:
- **'\*_res.rds'** files contain differential expression analysis results. They
are different for each tool and might be of interest only for users who
......@@ -127,9 +128,12 @@ Installs all required R packages.\
`Rscript install.R`
- **run.R** \
- **run.R countmatrix annotation output [-s] [-n top]** \
Contains all the pipeline. It needs three command arguments - count
matrix file name, table annotation file name and output directory name.
matrix file name **countmatrix**, table **annotation** file name and output directory name **output**.\
Options:\
**-s** allows to save extra information (see output)\
**-n top** allows to set **top** number of genes in signature.\
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**,
......@@ -138,48 +142,6 @@ Imports functions from **source/DESeq.R**, **source/EBSeq.R**,
`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. \
**Example**:
`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. \
**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`
- **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.
**Example**:
`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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"LOC100506421","-","+","+","-","-",2
"SLC13A2","-","+","+","-","-",2
"HPN","-","-","-","+","+",2
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"COL2A1","-","-","-","+","-",1
"AMACR","-","-","-","+","-",1
"KRT13","-","-","-","+","-",1
"PDK4","-","-","-","+","-",1
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"OR51E2","-","-","-","+","-",1
"ACSM1","-","-","-","+","-",1
"RPPH1","-","-","-","+","-",1
"C2orf88","-","-","-","-","+",1
"APOBEC3C","-","-","-","-","+",1
"CA14","-","-","-","-","+",1
"QPRT","-","-","-","-","+",1
"NKX2-3","-","-","-","-","+",1
"C8orf84","-","-","-","-","+",1
"PYCR1","-","-","-","-","+",1
"KCNJ15","-","-","-","-","+",1
"PIK3C2G","-","-","-","-","+",1
"MARCKSL1","-","-","-","-","+",1
"PHYHIPL","-","-","-","-","+",1
"TMLHE","-","-","-","-","+",1
"PCP4L1","-","-","-","-","+",1
"GPX2","-","-","-","-","+",1
"AOX1","-","-","-","-","+",1
"ANGPT1","-","-","-","-","+",1
"SIM2","-","-","-","-","+",1
"GNAO1","-","-","-","-","+",1
"LOC100127983","-","-","-","-","+",1
"PPARGC1A","-","-","-","-","+",1
"GSTM2P1","-","-","-","-","+",1
"RAB9B","-","-","-","-","+",1
"NECAB1","-","-","-","-","+",1
"LGR6","-","-","-","-","+",1
"EFNB1","-","-","-","-","+",1
"DESeq","voom","NOISeq","edgeR","EBSeq"
"MFSD2A","-","+","+","-"
"SERPINA5","+","+","+","+"
"ACSL6","-","-","-","-"
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"MCF2","+","-","-","-"
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"CLDN2","-","+","+","+"
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"NDRG4","-","-","-","-"
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"PATE2","-","-","-","-"
"TMEM114","-","-","+","+"
"CRTAC1","+","-","-","-"
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"KCP","-","-","-","-"
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"PIP","-","+","+","+"
"ANXA13","-","-","-","-"
"CA2","-","-","-","-"
"ABCG2","-","-","-","-"
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"DESeq" "EBSeq" "edgeR" "NOISeq" "voom" "count"
"SERPINA5" "+" "+" "+" "+" "+" 5
"CLDN2" "+" "+" "+" "+" "-" 4
"SPINK2" "+" "+" "+" "+" "-" 4
"AQP2" "+" "+" "+" "+" "-" 4
"PIP" "+" "+" "+" "+" "-" 4
"MFSD2A" "+" "-" "+" "+" "-" 3
"EMX2" "+" "+" "+" "-" "-" 3
"HOXB8" "+" "+" "+" "-" "-" 3
"EMX2OS" "+" "+" "+" "-" "-" 3
"TMEM114" "+" "+" "+" "-" "-" 3
"SEMG1" "-" "+" "+" "+" "-" 3
"PAEP" "-" "+" "+" "+" "-" 3
"SEMG2" "-" "+" "+" "+" "-" 3
"PATE4" "-" "+" "+" "+" "-" 3
"PATE1" "-" "+" "+" "+" "-" 3
"MCF2" "+" "-" "-" "-" "+" 2
"AKR1B1" "+" "-" "-" "+" "-" 2
"CRTAC1" "+" "-" "-" "-" "+" 2
"SEMA5B" "+" "-" "-" "+" "-" 2
"SLC2A9" "+" "-" "-" "-" "+" 2
"EDDM3A" "-" "+" "+" "-" "-" 2
"EDDM3B" "-" "+" "+" "-" "-" 2
"CRISP1" "-" "+" "+" "-" "-" 2
"DEFB125" "-" "+" "+" "-" "-" 2
"DEFB131" "-" "+" "+" "-" "-" 2
"GRXCR1" "-" "+" "+" "-" "-" 2
"POU3F3" "-" "+" "+" "-" "-" 2
"SPINT3" "-" "+" "+" "-" "-" 2
"SCGB1D4" "-" "+" "+" "-" "-" 2
"DEFB129" "-" "+" "+" "-" "-" 2
"SULT2A1" "-" "+" "+" "-" "-" 2
"WFDC9" "-" "+" "+" "-" "-" 2
"LOC100506421" "-" "+" "+" "-" "-" 2
"SLC13A2" "-" "+" "+" "-" "-" 2
"HPN" "-" "-" "-" "+" "+" 2
"ACSL6" "+" "-" "-" "-" "-" 1
"PKD1L2" "+" "-" "-" "-" "-" 1
"KLHL14" "+" "-" "-" "-" "-" 1
"MIR4508" "+" "-" "-" "-" "-" 1
"NDRG4" "+" "-" "-" "-" "-" 1
"SPINK13" "+" "-" "-" "-" "-" 1
"RASL10B" "+" "-" "-" "-" "-" 1
"PATE2" "+" "-" "-" "-" "-" 1
"CYP19A1" "+" "-" "-" "-" "-" 1
"LOC375295" "+" "-" "-" "-" "-" 1
"KCP" "+" "-" "-" "-" "-" 1
"ANO1" "+" "-" "-" "-" "-" 1
"ANXA13" "+" "-" "-" "-" "-" 1
"CA2" "+" "-" "-" "-" "-" 1
"ABCG2" "+" "-" "-" "-" "-" 1
"DEFB127" "-" "+" "-" "-" "-" 1
"DEFB112" "-" "+" "-" "-" "-" 1
"LCN1" "-" "-" "+" "-" "-" 1
"MUC6" "-" "-" "-" "+" "-" 1
"PCA3" "-" "-" "-" "+" "-" 1
"CYP4F8" "-" "-" "-" "+" "-" 1
"RMRP" "-" "-" "-" "+" "-" 1
"SLC26A3" "-" "-" "-" "+" "-" 1
"SLPI" "-" "-" "-" "+" "-" 1
"COL2A1" "-" "-" "-" "+" "-" 1
"AMACR" "-" "-" "-" "+" "-" 1
"KRT13" "-" "-" "-" "+" "-" 1
"PDK4" "-" "-" "-" "+" "-" 1
"TFF3" "-" "-" "-" "+" "-" 1
"PTGS2" "-" "-" "-" "+" "-" 1
"STAC2" "-" "-" "-" "+" "-" 1
"OR51E2" "-" "-" "-" "+" "-" 1
"ACSM1" "-" "-" "-" "+" "-" 1
"RPPH1" "-" "-" "-" "+" "-" 1
"C2orf88" "-" "-" "-" "-" "+" 1
"APOBEC3C" "-" "-" "-" "-" "+" 1
"CA14" "-" "-" "-" "-" "+" 1
"QPRT" "-" "-" "-" "-" "+" 1
"NKX2-3" "-" "-" "-" "-" "+" 1
"C8orf84" "-" "-" "-" "-" "+" 1
"PYCR1" "-" "-" "-" "-" "+" 1
"KCNJ15" "-" "-" "-" "-" "+" 1
"PIK3C2G" "-" "-" "-" "-" "+" 1
"MARCKSL1" "-" "-" "-" "-" "+" 1
"PHYHIPL" "-" "-" "-" "-" "+" 1
"TMLHE" "-" "-" "-" "-" "+" 1
"PCP4L1" "-" "-" "-" "-" "+" 1
"GPX2" "-" "-" "-" "-" "+" 1
"AOX1" "-" "-" "-" "-" "+" 1
"ANGPT1" "-" "-" "-" "-" "+" 1
"SIM2" "-" "-" "-" "-" "+" 1
"GNAO1" "-" "-" "-" "-" "+" 1
"LOC100127983" "-" "-" "-" "-" "+" 1
"PPARGC1A" "-" "-" "-" "-" "+" 1
"GSTM2P1" "-" "-" "-" "-" "+" 1
"RAB9B" "-" "-" "-" "-" "+" 1
"NECAB1" "-" "-" "-" "-" "+" 1
"LGR6" "-" "-" "-" "-" "+" 1
"EFNB1" "-" "-" "-" "-" "+" 1
"DESeq" "voom" "NOISeq" "edgeR" "EBSeq"
"MFSD2A" "-" "+" "+" "-"
"SERPINA5" "+" "+" "+" "+"
"ACSL6" "-" "-" "-" "-"
"PKD1L2" "-" "-" "-" "-"
"MCF2" "+" "-" "-" "-"
"EMX2" "-" "-" "+" "+"
"HOXB8" "-" "-" "+" "+"
"CLDN2" "-" "+" "+" "+"
"AKR1B1" "-" "+" "-" "-"
"SPINK2" "-" "+" "+" "+"
"KLHL14" "-" "-" "-" "-"
"MIR4508" "-" "-" "-" "-"
"EMX2OS" "-" "-" "+" "+"
"NDRG4" "-" "-" "-" "-"
"SPINK13" "-" "-" "-" "-"
"RASL10B" "-" "-" "-" "-"
"PATE2" "-" "-" "-" "-"
"TMEM114" "-" "-" "+" "+"
"CRTAC1" "+" "-" "-" "-"
"CYP19A1" "-" "-" "-" "-"
"SEMA5B" "-" "+" "-" "-"
"LOC375295" "-" "-" "-" "-"
"KCP" "-" "-" "-" "-"
"SLC2A9" "+" "-" "-" "-"
"AQP2" "-" "+" "+" "+"
"ANO1" "-" "-" "-" "-"
"PIP" "-" "+" "+" "+"
"ANXA13" "-" "-" "-" "-"
"CA2" "-" "-" "-" "-"
"ABCG2" "-" "-" "-" "-"
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