Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
B
BSseqMethDiffAnalysis
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Package Registry
Container Registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Terms and privacy
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Chloe Cerutti
BSseqMethDiffAnalysis
Commits
764f226f
Commit
764f226f
authored
2 years ago
by
Chloe Cerutti
Browse files
Options
Downloads
Patches
Plain Diff
Update Readme
parent
f50544b2
No related branches found
Branches containing commit
No related tags found
Tags containing commit
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
README.md
+35
-28
35 additions, 28 deletions
README.md
with
35 additions
and
28 deletions
README.md
+
35
−
28
View file @
764f226f
...
...
@@ -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
```
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment