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Commit 764f226f authored by Chloe Cerutti's avatar Chloe Cerutti
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Update Readme

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......@@ -108,20 +108,27 @@ Options:
```sh
Rscript ../bsseqmethdiffanalysis/DSS/MethDiffDSS.R \
-d "path to preprocessed file (eg: outpout_dir/bismark_format)" \
-f file1.tsv,file2.tsv \ # all library file names separated with comma
--pool1 7127emb08_bismark.tsv \ # all library file names of condition 1 separated with comma
--pool2 7127emb15_bismark.tsv \ # all library file names of condition 2 separated with comma
--dmr TRUE \
--dmr.type qvalue \ # dmr stats (pvalue or qvalue)
--gff annotation_file.gtf \
--type 'gene,exon,five_prime_utr,three_prime_utr' \ # type of annotation to loock for in gff file
--tss tss.txt \ # List of TSS (files format: chr\ttss\tstrand)
--plots TRUE \ # output plot boolean
-o many_test/diff_median_qvalue_20_04_2/ \ # Ouput directory for plots and Rfiles
--dmr.numC 1 \ # minimum number of dmc for one dmr
--alpha=0.2 \ #significance level of the tests (i.e. acceptable rate of false-positive in the list of DMC)
--dmr.propDMC 0.5 # cutoff of the proportion of DMCs in each region to call DMR
-d "path to preprocessed file (eg: outpout_dir/bismark_format)" \
-m "File of summarized data and experience" \
--smoothing TRUE \
--formula "line+sex" \
--term "line,sex" \
--ref "epi-,F" \
--dmr TRUE \
--dmr.type qvalue \ # dmr stats (pvalue or qvalue)
--dmr.numC 3 \ # minimum number of dmc for one dmr
--dmr.propDMC 0.5 \ # cutoff of the proportion of DMCs in each region to call DMR
--alpha 0.05 \ # significance level of the tests (i.e. acceptable rate of false-positive in the list of DMC)
--correct BH \
--type 'gene,exon,five_prime_utr,three_prime_utr' \ # type of annotation to loock for in gff file
--tss tss.txt \ # List of TSS (files format: chr\ttss\tstrand)
--gff annotation_file.gtf \
--parallel TRUE \
--ncores 16 \
--plots TRUE \ # output plot boolean
--rda FALSE \
-o output_directory/ \ # Ouput directory for plots and Rfiles
--process_functions ../bsseqmethdiffanalysis/DSS/BS_DSS_analysis.R
```
......@@ -329,20 +336,20 @@ Options:
```sh
Rscript ../bsseqmethdiffanalysis/edgeR/MethDiffDSS.R \
-d "path to preprocessed file (eg: outpout_dir/bismark_format)" \
-m "File of summarized data and experience" \
--multifactor TRUE \
--formula "treat+sex" \
--ref "T,F" \
--term "treat,sex" \
--parallel TRUE \
--ncores 16 \
-o output_directory/ \ # Ouput directory for plots and Rfiles
--dmr TRUE \
--dmr.numC 3 \ # minimum number of dmc for one dmr
--dmr.propDMC 0.5 \ # cutoff of the proportion of DMCs in each region to call DMR
--alpha 0.05 \ #significance level of the tests (i.e. acceptable rate of false-positive in the list of DMC)
--plot TRUE # output plot boolean
-d "path to preprocessed file (eg: outpout_dir/bismark_format)" \
-m "File of summarized data and experience" \
--multifactor TRUE \
--formula "treat+sex" \
--ref "T,F" \
--term "treat,sex" \
--parallel TRUE \
--ncores 16 \
-o output_directory/ \ # Ouput directory for plots and Rfiles
--dmr TRUE \
--dmr.numC 3 \ # minimum number of dmc for one dmr
--dmr.propDMC 0.5 \ # cutoff of the proportion of DMCs in each region to call DMR
--alpha 0.05 \ #significance level of the tests (i.e. acceptable rate of false-positive in the list of DMC)
--plot TRUE # output plot boolean
```
......
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