https://sourceforge.net/p/mageck/wiki/usage/Recent changes to usageenMon, 01 Jul 2019 17:43:04 -0000https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v52 +++ v53 @@ -29,10 +29,10 @@ usage: mageck test [-h] -k COUNT_TABLE (-t TREATMENT_ID | --day0-label DAY0_LABEL) [-c CONTROL_ID] - [--norm-method {none,median,total,control}] + [--paired] [--norm-method {none,median,total,control}] [--gene-test-fdr-threshold GENE_TEST_FDR_THRESHOLD] [--adjust-method {fdr,holm,pounds}] - [--variance-from-all-samples] + [--variance-estimation-samples VARIANCE_ESTIMATION_SAMPLES] [--sort-criteria {neg,pos}] [--remove-zero {none,control,treatment,both,any}] [--remove-zero-threshold REMOVE_ZERO_THRESHOLD] @@ -59,10 +59,11 @@ -----------------|------------ -h, --help | show this help message and exit -c CONTROL_ID, --control-id CONTROL_ID | Sample label or sample index in the count table as control experiments, separated by comma (,). Default is all the samples not specified in treatment experiments. See [input/#sample-index](input/#sample-index) for a detailed description. +--paired|Paired sample comparisons. In this mode, the number of samples in -t and -c must match and have an exact order in terms of samples. For example, "-t HL60.final,KBM7.final -c HL60.initial,KBM7.initial". --norm-method {none,median,total,control} | Method for normalization, default median. If control is specified, the size factor will be estimated using control sgRNAs specified in --control-sgrna option. --gene-test-fdr-threshold GENE_TEST_FDR_THRESHOLD | FDR threshold for gene test, default 0.25. --adjust-method {fdr,holm,pounds}| Method for sgrna-level p-value adjustment, including false discovery rate (fdr), holm's method (holm), or pounds's method (pounds). ---variance-from-all-samples | Estimate the variance from all samples, instead of from only control samples. Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples. + --variance-estimation-samples VARIANCE_ESTIMATION_SAMPLES|Sample label or sample index for estimating variances, separated by comma (,). See -t/--treatment-id option for specifying samples. --sort-criteria {neg,pos} | Sorting criteria, either by negative selection (neg) or positive selection (pos). Default negative selection. --remove-zero {none,control,treatment,both}|Whether to remove zero-count sgRNAs in control and/or treatment experiments. Default: none (do not remove those zero-count sgRNAs). --pdf-report|Generate pdf report of the analysis. </pre> </div>Wei LiMon, 01 Jul 2019 17:43:04 -0000https://sourceforge.net26de202aeb38604b6303f9aaece87ade428b51b2https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v51 +++ v52 @@ -323,7 +323,7 @@ ## mageckGSEA ## -mageckGSEA is a fast implementation of Gene Set Enrichment Analysis (GSEA). It's used by MAGeCK for quality controls and pathway enrichment tests. +mageckGSEA is a fast implementation of Gene Set Enrichment Analysis (GSEA) using C++. It's used by MAGeCK for quality controls and pathway enrichment tests. Compared with the official GSEA program, the main advantage is its easy use and extremely fast running speed. In the *gsea/demo* folder, an example is provided to run GSEA. Use the following command to perform GSEA analysis based on the ranked gene list in demo1.txt (provided in the demo folder), tested on pathways defined in kegg.ribosome.gmt (provided in the demo folder). The scores on the 2nd column will be used to rank genes (-c 1), and permute 10000 times to get p value: </pre> </div>Wei LiThu, 12 Jul 2018 20:31:04 -0000https://sourceforge.net9036841aa820f962c313bc337e8c6dc5349c55c3https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v50 +++ v51 @@ -326,10 +326,56 @@ mageckGSEA is a fast implementation of Gene Set Enrichment Analysis (GSEA). It's used by MAGeCK for quality controls and pathway enrichment tests. -In the *gsea/demo* folder, an example is provided to run GSEA. Use the following command to perform GSEA analysis based on the ranked gene list in demo1.txt (provided in the demo folder), tested on pathways defined in kegg.ribosome.gmt (provided in the demo folder), and permute 100000 times to get p value: +In the *gsea/demo* folder, an example is provided to run GSEA. Use the following command to perform GSEA analysis based on the ranked gene list in demo1.txt (provided in the demo folder), tested on pathways defined in kegg.ribosome.gmt (provided in the demo folder). The scores on the 2nd column will be used to rank genes (-c 1), and permute 10000 times to get p value: ::bash - mageckGSEA -r demo1.txt -g kegg.ribosome.gmt -p 10000 + mageckGSEA -r demo1.txt -g kegg.ribosome.gmt -c 1 -p 10000 + +You can either provide genes with their scores, as is in demo1.txt (genes with smaller scores are ranked in the front). + + + ::bash + SYNRG 0.715581582 + SREK1 0.992306809 + SLC25A46 0.057411873 + COL4A5 0.36387645 + CCDC22 -0.463887932 + MVD 0.020897922 + + +mageckGSEA will first rank genes based on the provided scores, as long as you indicate which column to use (-c 1). + +Or you can just provide gene rankings, as is in demo2.txt. + + ::bash + C5orf64 + TTC17 + MRPS27 + PIGY + GPAA1 + KIF4A + EPS15 + +The output is a tab-separated file to report the following statistics of GSEA: + + + Pathway Size ES p p_permutation FDR Ranking Hits LFC + KEGG_RIBOSOME 88 0.3262 0.00240772 0.0043 0.0043 0 32 0 + + + +Item|Explanation +--------|------------- +Pathway | The name of the pathway +Size|The size of the pathway, i.e., the number of genes +ES|Enrichment Score (ES) in GSEA +p|The p value of ES +p_permutation|The permutation p value of ES (usually more accurate than p +FDR|False Discovery Rate of p_permutation +Ranking|The ranking of this pathway +Hits|The number of genes that are ranked before ES score. See "Leading Edge" analysis of GSEA +LFC|Log fold change (not implemented) + </pre> </div>Wei LiThu, 12 Jul 2018 20:14:53 -0000https://sourceforge.net06820911f23afc3e9db9b51da833b32bf609b1behttps://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v49 +++ v50 @@ -155,7 +155,6 @@ ## pathway ## MAGeCK can also invoke GSEA (default) or RRA to test if a pathway is enriched in one particular gene ranking. - *usage*: @@ -327,6 +326,13 @@ mageckGSEA is a fast implementation of Gene Set Enrichment Analysis (GSEA). It's used by MAGeCK for quality controls and pathway enrichment tests. +In the *gsea/demo* folder, an example is provided to run GSEA. Use the following command to perform GSEA analysis based on the ranked gene list in demo1.txt (provided in the demo folder), tested on pathways defined in kegg.ribosome.gmt (provided in the demo folder), and permute 100000 times to get p value: + + ::bash + mageckGSEA -r demo1.txt -g kegg.ribosome.gmt -p 10000 + + + USAGE: ::bash @@ -341,7 +347,7 @@ ----------------------------------------|------------------ -e, --reverse_value | Reverse the order of the gene. -s, --sort_byp | Sort the pathways by p value. --c score_column, --score_column score_column | The column for gene scores. If you just want to use the ranking of the gene (located at the 1st column), use 0. The column number starts from 0. Default: 0. +-c score_column, --score_column score_column | The column for gene scores. If you just want to use the ranking of the gene (located at the 1st column), use 0. Otherwise, specify which column should be used to rank the gene. The column number starts from 0. Default: 0. -p perm_time, --perm_time perm_time | Permutations, default 1000. -n pathway_name, --pathway_name pathway_name | Name of the pathway to be tested. If not found, will test all pathways. -o output_file, --output_file output_file | The name of the output file. Use - to print to standard output. </pre> </div>Wei LiThu, 12 Jul 2018 19:47:18 -0000https://sourceforge.net9f95d2c6f2de14b50e67dfbaf034836871b43927https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v48 +++ v49 @@ -154,7 +154,7 @@ ## pathway ## -MAGeCK can also invoke RRA to test if a pathway is enriched in one particular gene ranking. +MAGeCK can also invoke GSEA (default) or RRA to test if a pathway is enriched in one particular gene ranking. *usage*: </pre> </div>Wei LiThu, 12 Jul 2018 19:39:51 -0000https://sourceforge.netfafbde7a866206b150c60c28789dd3af0f76164fhttps://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v47 +++ v48 @@ -74,7 +74,7 @@ Parameter | Explanation -----------------|------------ -n OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX | The prefix of the output file(s). Default sample1. ---control-sgrna CONTROL_SGRNA | A list of control sgRNAs for normalization and for generating the null distribution of RRA. +--control-sgrna CONTROL_SGRNA | A list of control sgRNAs for normalization and for generating the null distribution of RRA. See the [format specification](https://sourceforge.net/p/mageck/wiki/input/#negative-control-sgrna-list). --normcounts-to-file | Write normalized read counts to file ({output-prefix}.normalized.txt). --keep-tmp | Keep intermediate files. --skip-gene SKIP_GENE | Skip genes in the report. By default, "NA" or "na" will be skipped. @@ -121,7 +121,7 @@ Parameter | Explanation -----------------|------------ --norm-method {none,median,total,control}| Method for normalization, including "none" (no normalization), "median" (median normalization, default), "total" (normalization by total read counts), "control" (normalization by control sgRNAs specified by the --control-sgrna option). ---control-sgrna CONTROL_SGRNA| A list of control sgRNAs for normalization and for generating the null distribution of RRA. +--control-sgrna CONTROL_SGRNA| A list of control sgRNAs for normalization and for generating the null distribution of RRA. See the [format specification](https://sourceforge.net/p/mageck/wiki/input/#negative-control-sgrna-list). **optional arguments for input and output**: @@ -231,7 +231,7 @@ -n OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX| The prefix of the output file(s). Default sample1. -i INCLUDE_SAMPLES, --include-samples INCLUDE_SAMPLES | Specify the sample labels if the design matrix is not given by file in the --design-matrix option. Sample labels are separated by ",", and must match the labels in the count table. -b BETA_LABELS, --beta-labels BETA_LABELS | Specify the labels of the variables (i.e., beta), if the design matrix is not given by file in the --design-matrix option. Should be separated by ",", and the number of labels must equal to (# columns of design matrix), including baseline labels. Default value: "bata_0,beta_1,beta_2,...". ---control-sgrna CONTROL_SGRNA | A list of control sgRNAs. +--control-sgrna CONTROL_SGRNA | A list of control sgRNAs. See the [format specification](https://sourceforge.net/p/mageck/wiki/input/#negative-control-sgrna-list). **Optional arguments for CNV correction:** </pre> </div>Wei LiSun, 20 May 2018 16:10:29 -0000https://sourceforge.netb3731e3aff88c34fa68a8bfff259fa14d952ada6https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v46 +++ v47 @@ -196,20 +196,24 @@ *usage*: - usage: mageck mle [-h] -k COUNT_TABLE - (-d DESIGN_MATRIX | --day0-label DAY0_LABEL) - [-n OUTPUT_PREFIX] [-i INCLUDE_SAMPLES] [-b BETA_LABELS] - [--control-sgrna CONTROL_SGRNA] [--cnv-norm CNV_NORM] - [--debug] [--debug-gene DEBUG_GENE] - [--norm-method {none,median,total,control}] - [--genes-varmodeling GENES_VARMODELING] - [--permutation-round PERMUTATION_ROUND] [--remove-outliers] - [--threads THREADS] [--adjust-method {fdr,holm,pounds}] - [--sgrna-efficiency SGRNA_EFFICIENCY] - [--sgrna-eff-name-column SGRNA_EFF_NAME_COLUMN] - [--sgrna-eff-score-column SGRNA_EFF_SCORE_COLUMN] - [--update-efficiency] [--bayes] [-p] [-w PPI_WEIGHTING] - [-e NEGATIVE_CONTROL] + usage: mageck.beta mle [-h] -k COUNT_TABLE + (-d DESIGN_MATRIX | --day0-label DAY0_LABEL) + [-n OUTPUT_PREFIX] [-i INCLUDE_SAMPLES] + [-b BETA_LABELS] [--control-sgrna CONTROL_SGRNA] + [--cnv-norm CNV_NORM] [--cnv-est CNV_EST] [--debug] + [--debug-gene DEBUG_GENE] + [--norm-method {none,median,total,control}] + [--genes-varmodeling GENES_VARMODELING] + [--permutation-round PERMUTATION_ROUND] + [--no-permutation-by-group] + [--max-sgrnapergene-permutation MAX_SGRNAPERGENE_PERMUTATION] + [--remove-outliers] [--threads THREADS] + [--adjust-method {fdr,holm,pounds}] + [--sgrna-efficiency SGRNA_EFFICIENCY] + [--sgrna-eff-name-column SGRNA_EFF_NAME_COLUMN] + [--sgrna-eff-score-column SGRNA_EFF_SCORE_COLUMN] + [--update-efficiency] [--bayes] [-p] [-w PPI_WEIGHTING] + [-e NEGATIVE_CONTROL] **required arguments**: @@ -228,8 +232,12 @@ -i INCLUDE_SAMPLES, --include-samples INCLUDE_SAMPLES | Specify the sample labels if the design matrix is not given by file in the --design-matrix option. Sample labels are separated by ",", and must match the labels in the count table. -b BETA_LABELS, --beta-labels BETA_LABELS | Specify the labels of the variables (i.e., beta), if the design matrix is not given by file in the --design-matrix option. Should be separated by ",", and the number of labels must equal to (# columns of design matrix), including baseline labels. Default value: "bata_0,beta_1,beta_2,...". --control-sgrna CONTROL_SGRNA | A list of control sgRNAs. ---cnv-norm CNV_NORM | A matrix of copy number variation data across cell lines to normalize CNV-biased BetaScores. - + +**Optional arguments for CNV correction:** + +Parameter | Explanation +-----------------|------------ +--cnv-norm CNV_NORM | A matrix of copy number variation data across cell lines to normalize CNV-biased sgRNA scores prior to gene ranking. **optional arguments for MLE module**: @@ -240,7 +248,9 @@ --debug-gene DEBUG_GENE| Debug mode to only run one gene with specified ID. --norm-method {none,median,total,control} | Method for normalization, including "none" (no normalization), "median" (median normalization, default), "total" (normalization by total read counts), "control" (normalization by control sgRNAs specified by the --control-sgrna option). --genes-varmodeling GENES_VARMODELING| The number of genes for mean-variance modeling. Default 1000. ---permutation-round PERMUTATION_ROUND| The rounds for permutation (interger). The permutation time is (# genes) \* x for x rounds of permutation. Suggested value: 100 (may take longer time). Default 10. +--permutation-round PERMUTATION_ROUND| The rounds for permutation (interger). The permutation time is (# genes) \* x for x rounds of permutation. Suggested value: 10 (may take longer time). Default 2. +--no-permutation-by-group| By default, gene permutation is performed separately, by their number of sgRNAs. Turning this option will perform permutation on all genes together. This makes the program faster, but the p value estimation is accurate only if the number of sgRNAs per gene is approximately the same. +--max-sgrnapergene-permutation MAX_SGRNAPERGENE_PERMUTATION| Only permute genes by group if the number of sgRNAs per gene is smaller than this number. This will save a lot of time if some regions are targeted by a large number of sgRNAs (usually hundreds). Must be an integer. Default 100. --remove-outliers | Try to remove outliers. Turning this option on will slow the algorithm. --threads THREADS|Using multiple threads to run the algorithm. Default using only 1 thread. --adjust-method {fdr,holm,pounds} | Method for sgrna-level p-value adjustment, including false discovery rate (fdr), holm's method (holm), or pounds's method (pounds). @@ -253,6 +263,9 @@ --sgrna-eff-name-column SGRNA_EFF_NAME_COLUMN|The sgRNA ID column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 0 (the first column). --sgrna-eff-score-column SGRNA_EFF_SCORE_COLUMN|The sgRNA efficiency prediction column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 1 (the second column). --update-efficiency | Iteratively update sgRNA efficiency during EM iteration. + + + ## plot ## </pre> </div>Wei LiSat, 06 Jan 2018 04:27:40 -0000https://sourceforge.net238702464f7a72034fae1fd9ebff2066d6d0b4a8https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v45 +++ v46 @@ -26,7 +26,7 @@ *usage*: - usage: mageck test [-h] -k COUNT_TABLE + usage: mageck test [-h] -k COUNT_TABLE (-t TREATMENT_ID | --day0-label DAY0_LABEL) [-c CONTROL_ID] [--norm-method {none,median,total,control}] </pre> </div>Wei LiSat, 06 Jan 2018 04:23:00 -0000https://sourceforge.net04a3df2aa9adda452ea0e6e3baad4813c506f18bhttps://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v44 +++ v45 @@ -26,16 +26,23 @@ *usage*: - usage: mageck test [-h] -k COUNT_TABLE (-t TREATMENT_ID | --day0-label DAY0_LABEL) [-c CONTROL_ID] - [-n OUTPUT_PREFIX] [--norm-method {none,median,total,control}] - [--normcounts-to-file] - [--gene-test-fdr-threshold GENE_TEST_FDR_THRESHOLD] - [--adjust-method {fdr,holm}] [--variance-from-all-samples] - [--sort-criteria {neg,pos}] [--keep-tmp] - [--control-sgrna CONTROL_SGRNA] - [--remove-zero {none,control,treatment,both}] - [--gene-lfc-method {median,alphamedian,mean,alphamean,secondbest}] - [--pdf-report] + usage: mageck test [-h] -k COUNT_TABLE + (-t TREATMENT_ID | --day0-label DAY0_LABEL) + [-c CONTROL_ID] + [--norm-method {none,median,total,control}] + [--gene-test-fdr-threshold GENE_TEST_FDR_THRESHOLD] + [--adjust-method {fdr,holm,pounds}] + [--variance-from-all-samples] + [--sort-criteria {neg,pos}] + [--remove-zero {none,control,treatment,both,any}] + [--remove-zero-threshold REMOVE_ZERO_THRESHOLD] + [--pdf-report] + [--gene-lfc-method {median,alphamedian,mean,alphamean,secondbest}] + [-n OUTPUT_PREFIX] [--control-sgrna CONTROL_SGRNA] + [--normcounts-to-file] [--skip-gene SKIP_GENE] + [--keep-tmp] + [--additional-rra-parameters ADDITIONAL_RRA_PARAMETERS] + [--cnv-norm CNV_NORM] [--cell-line CELL_LINE] **required arguments**: @@ -72,6 +79,11 @@ --keep-tmp | Keep intermediate files. --skip-gene SKIP_GENE | Skip genes in the report. By default, "NA" or "na" will be skipped. --additional-rra-parameters ADDITIONAL_RRA_PARAMETERS | Additional arguments to run RRA. They will be appended to the command line for calling RRA. + +**Optional arguments for CNV correction:** + +Parameter | Explanation +-----------------|------------ --cnv-norm CNV_NORM | A matrix of copy number variation data across cell lines to normalize CNV-biased sgRNA scores prior to gene ranking. --cell-line CELL_LINE | The name of the cell line to be used for copy number variation normalization. </pre> </div>Wei LiSat, 06 Jan 2018 04:22:20 -0000https://sourceforge.net0ac72addcf10191edc9caff784caa9debbc91780https://sourceforge.net/p/mageck/wiki/usage/<div class="markdown_content"><pre>--- v43 +++ v44 @@ -305,9 +305,10 @@ USAGE: ::bash - mageckGSEA [-e] [-s] [-c score_column] [-p perm_time] [-n - pathway_name] [-o output_file] -r rank_file -g - gmt_file [--] [--version] [-h] + mageckGSEA -r rank_file -g gmt_file + [-e] [-s] [-c score_column] + [-p perm_time] [-n pathway_name] + [-o output_file] [--] [--version] [-h] </pre> </div>Wei LiWed, 17 May 2017 19:53:36 -0000https://sourceforge.net385598f28f4215687c83e82907d76ec8cb61f1f5