From 1ae0a803055fece1c37a0ff84614b54200280062 Mon Sep 17 00:00:00 2001 From: ytakemon Date: Thu, 2 Nov 2017 14:51:01 -0400 Subject: [PATCH 1/5] Clarifying datasets: list vs elements --- docs/QTLViewerDataStructures.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/QTLViewerDataStructures.md b/docs/QTLViewerDataStructures.md index 6de9289..be6cff3 100644 --- a/docs/QTLViewerDataStructures.md +++ b/docs/QTLViewerDataStructures.md @@ -17,7 +17,7 @@ The following sections try to explain what each element is required and which is The following elements should be in the `RData` file. * [`genome.build`](#genome_build) - string specifying the genome build -* [`genoprobs`](#genoprobs) - the genotype probabilities +* [`genoprobs`](#genoprobs) - the genotype probabilities * [`K`](#kinship) - the kinship matrix * [`map`](#map) - list of one element per chromosome, with the genomic position of each marker * [`markers`](#markers) - marker names and positions @@ -66,7 +66,7 @@ Please see the documentation at [R/qtl2geno](https://github.com/rqtl/qtl2geno). - **R data type:** [data.frame](http://www.r-tutor.com/r-introduction/data-frame) -- **Description:** marker information +- **Description:** marker information The following column names must be present: @@ -80,24 +80,24 @@ The following column names must be present: ------------ -## Configurable Elements +## Configurable `dataset.*` lists -The following element is a *special* element and there must be at least per `RData` file. +The `dataset.*` is a *special* [list](http://www.r-tutor.com/r-introduction/list), and there must be at least one per `RData` file. Each `dataset.*` contains elements pertaining to either mRNA, protein, or phenotype. * [`dataset.*`](#data_elements) - special element -**mRNA**, **protein**, and **phenotype** data sets CAN be configured by `dataset.*` elements. +**mRNA**, **protein**, and **phenotype** datasets CAN be configured by `dataset.*` lists. ### `dataset.*` - **R data type:** [list](http://www.r-tutor.com/r-introduction/list) -- **Description:** annotations for **mRNA** or **protein** -The `*` part should be alpha-numeric text (underscores are allowed) that describes succinctly your data element. There must be at least 1 `dataset.*` elements per `RData` file. These elements will allow you to store multiple **mRNA**, **protein**, and **phenotype** data sets. For example, there could be `dataset.mRNA` and `dataset.mRNA2` to store 2 mRNA datasets. The text for the `*` part should be any text that make sense to you or your dataset. What is defined in the `dataset.*` element is what is more important. +- **Description:** annotations for **mRNA** or **protein** related `dataset.*` lists. +The `*` part should be alpha-numeric text (underscores are allowed) that should be any text that makes sense to you or your dataset. There must be at least 1 `dataset.*` elements per `RData` file. These elements will allow you to store multiple **mRNA**, **protein**, and **phenotype** data sets. For example, there could be `dataset.mRNA` and `dataset.mRNA2` to store 2 mRNA datasets. What is defined in the `dataset.*` element is what is more important. ------------ -### mRNA and protein `dataset.*` +### mRNA and protein `dataset.*` elements The following elements should be in each **mRNA** and **protein** `dataset.*` [list](http://www.r-tutor.com/r-introduction/list) @@ -246,7 +246,7 @@ Extra columns can be included, and will be rendered in the viewer. For example, The following elements should be in each **phenotype** `dataset.*` [list](http://www.r-tutor.com/r-introduction/list). -* [`annots`](#pheno_annots) - data dictionary +* [`annots`](#pheno_annots) - data dictionary * [`covar`](#pheno_covar) - matrix of covariates data, samples (rows) x covariates (columns) * [`covar.factors`](#pheno_covar_factors) - specific information about the covars * [`datatype`](#pheno_datatype) - type of data, must be **phenotype** From 14114cc9f5f3e4bb5ca17d8f89317be11ebe707b Mon Sep 17 00:00:00 2001 From: ytakemon Date: Thu, 2 Nov 2017 14:52:16 -0400 Subject: [PATCH 2/5] Clarifying datasets list vs elements --- docs/QTLViewerDataStructures.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/QTLViewerDataStructures.md b/docs/QTLViewerDataStructures.md index be6cff3..2314176 100644 --- a/docs/QTLViewerDataStructures.md +++ b/docs/QTLViewerDataStructures.md @@ -112,6 +112,16 @@ The following elements should be in each **mRNA** and **protein** `dataset.*` [l * [`raw`](#mrna_raw) - matrix of raw mrna data (counts out of [EMASE](http://churchill-lab.github.io/emase/)) * [`samples`](#mrna_samples) - sample annotations +For example, once each element has been formatted accordingly, the elements should be consolidated in to the `dataset.*` via the following code: + +```CompileDataset +dataset.mrna <- c(“annots” = annots.mrna, + “covar” = covar, + "covar.factor" = covar.factors, + ...) +``` + + ------------ #### `annots` *REQUIRED* From 59f1a9b0e981ef2ae2298bac25a2cd4f34968c03 Mon Sep 17 00:00:00 2001 From: ytakemon Date: Thu, 2 Nov 2017 14:53:00 -0400 Subject: [PATCH 3/5] Fix typo --- docs/QTLViewerDataStructures.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/QTLViewerDataStructures.md b/docs/QTLViewerDataStructures.md index 2314176..e7fb7e1 100644 --- a/docs/QTLViewerDataStructures.md +++ b/docs/QTLViewerDataStructures.md @@ -117,7 +117,7 @@ For example, once each element has been formatted accordingly, the elements shou ```CompileDataset dataset.mrna <- c(“annots” = annots.mrna, “covar” = covar, - "covar.factor" = covar.factors, + "covar.factors" = covar.factors, ...) ``` From 3d31e9a801e30751ed13e9458f90cc1063f6c321 Mon Sep 17 00:00:00 2001 From: ytakemon Date: Thu, 2 Nov 2017 14:54:34 -0400 Subject: [PATCH 4/5] Fixing typo --- docs/QTLViewerDataStructures.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/QTLViewerDataStructures.md b/docs/QTLViewerDataStructures.md index e7fb7e1..01c8496 100644 --- a/docs/QTLViewerDataStructures.md +++ b/docs/QTLViewerDataStructures.md @@ -112,7 +112,7 @@ The following elements should be in each **mRNA** and **protein** `dataset.*` [l * [`raw`](#mrna_raw) - matrix of raw mrna data (counts out of [EMASE](http://churchill-lab.github.io/emase/)) * [`samples`](#mrna_samples) - sample annotations -For example, once each element has been formatted accordingly, the elements should be consolidated in to the `dataset.*` via the following code: +For example, once each element has been formatted accordingly, the elements can be compiled in to the `dataset.*` via the following code: ```CompileDataset dataset.mrna <- c(“annots” = annots.mrna, @@ -121,7 +121,6 @@ dataset.mrna <- c(“annots” = annots.mrna, ...) ``` - ------------ #### `annots` *REQUIRED* From f58fb2536094ec55f570e204b2dfda62e45a3f56 Mon Sep 17 00:00:00 2001 From: ytakemon Date: Tue, 7 Nov 2017 11:02:02 -0500 Subject: [PATCH 5/5] fixing code --- docs/QTLViewerDataStructures.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/QTLViewerDataStructures.md b/docs/QTLViewerDataStructures.md index 01c8496..ebd63a6 100644 --- a/docs/QTLViewerDataStructures.md +++ b/docs/QTLViewerDataStructures.md @@ -115,7 +115,7 @@ The following elements should be in each **mRNA** and **protein** `dataset.*` [l For example, once each element has been formatted accordingly, the elements can be compiled in to the `dataset.*` via the following code: ```CompileDataset -dataset.mrna <- c(“annots” = annots.mrna, +dataset.mrna <- list(“annots” = annots.mrna, “covar” = covar, "covar.factors" = covar.factors, ...)