From cb003058bbae4462df6221afa14da25217d3c4ee Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 6 Dec 2024 14:59:56 +0100 Subject: [PATCH 1/2] Updated usage docs with missing params --- CHANGELOG.md | 1 + docs/usage.md | 20 ++++++++++++++++++++ 2 files changed, 21 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d551f0c..7f76e624 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [#255](https://github.com/qbic-pipelines/rnadeseq/pull/255) Add usage docu for datasources, heatmaps_cluster_rows/cols and pathway_adj_pval_threshold params - [#251](https://github.com/qbic-pipelines/rnadeseq/pull/251) Get raw gene count tables from either Salmon and RSEM analysis - [#250](https://github.com/qbic-pipelines/rnadeseq/pull/250) Added clearer error message for incorrect contrast_pairs diff --git a/docs/usage.md b/docs/usage.md index 9e5da48f..818bc9cb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -34,6 +34,9 @@ - [`--vst_genes_number`](#--vst_genes_number) - [`--round_DE`](#--round_DE) - [`--run_pathway_analysis`](#--run_pathway_analysis) + - [`--pathway_adj_pval_threshold`](#--pathway_adj_pval_threshold) + - [`--heatmaps_cluster_rows`](#--heatmaps_cluster_rows) + - [`--heatmaps_cluster_cols`](#--heatmaps_cluster_cols) - [`--input_type`](#--input_type) - [`--multiqc`](#--multiqc) - [`--project_summary`](#--project_summary) @@ -48,6 +51,7 @@ - [`--custom_gmt`](#--custom_gmt) - [`--set_background`](#--set_background) - [`--custom_background`](#--custom_background) + - [`--datasources`](#--datasources) - [`--igenomes_base`](#--igenomes_base) - [`--igenomes_ignore`](#--igenomes_ignore) - [Job resources](#job-resources) @@ -373,6 +377,18 @@ Integer indicating to how many decimals to round the DE results (default: -1, in Set this flag to run pathway analysis, otherwise, this step will be skipped. +### `--pathway_adj_pval_threshold` + +Use this param to specifically set the adjusted p value threshold for pathway enrichment analysis (will otherwise use the same adjusted p value threshold as for the DE analysis, as set with the param `--adj_pval_threshold`). + +### `--heatmaps_cluster_rows` + +Use this flag to set whether the heatmaps of gene expression in enriched pathways should by clustered row-wise (default true). + +### `--heatmaps_cluster_cols` + +Use this flag to set whether the heatmaps of gene expression in enriched pathways should by clustered column-wise (default false). + ### `--input_type` This tells the pipeline which type of input dataset is provided. Must be one of 'featurecounts', 'rsem', 'salmon', 'smrnaseq', default: featurecounts. @@ -450,6 +466,10 @@ Whether to restrict pathway analysis to a background gene list (default: true, w Path to custom background TXT file with one gene ID per line to use as background genes, not necessary if `--run_pathway_analysis = false` or `--set_background = false`. +### `--datasources` + +Which datasources to use for pathway analysis, comma-separated string like 'KEGG,REAC'. See param 'sources' on https://rdrr.io/cran/gprofiler2/man/gost.html for a list of available sources. If not set, will use all sources. If set while a --custom_gmt is provided, will filter the GMT for these datasources (will not filter for the GO subtypes like GO:BP, just for GO). + ## Job resources ### Automatic resubmission From 8a994adfa966669afce73182b139064b41c6adfc Mon Sep 17 00:00:00 2001 From: WackerO Date: Mon, 9 Dec 2024 11:42:23 +0100 Subject: [PATCH 2/2] prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f76e624..4e28065d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,6 +34,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed - [#247](https://github.com/qbic-pipelines/rnadeseq/pull/247) Removed hard-coded comment about usage of gprofiler databases KEGG and REAC in the report + ## 2.3 - Flowering Orchards ### Added