Update Readme

README.md

@@ -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
 ```