From 4721db95d82e92b759e1079b884dc84fcf0f8710 Mon Sep 17 00:00:00 2001 From: Jasdeep Singh <55511370+singhomics@users.noreply.github.com> Date: Sun, 8 Nov 2020 01:34:45 +0530 Subject: [PATCH 1/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4088cb8..e807d94 100644 --- a/README.md +++ b/README.md @@ -1 +1 @@ -# Building out BiocSwirl interactive hands-on content on relevant bioinformatics tools, datasets, and pipelines +# Building out BiocSwirl interactive hands-on content on relevant bioinformatics tools, datasets, and pipeline From bd9a8f6fb2ba4d76a0e78b2d6bd9dcf67389c8e5 Mon Sep 17 00:00:00 2001 From: Jasdeep Singh Date: Sun, 8 Nov 2020 01:46:20 +0530 Subject: [PATCH 2/4] add_rmd --- GWAS.rmd | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 GWAS.rmd diff --git a/GWAS.rmd b/GWAS.rmd new file mode 100644 index 0000000..7c4bf9e --- /dev/null +++ b/GWAS.rmd @@ -0,0 +1,50 @@ +Using Genome Association and Prediction Integrated Tool (GAPIT) to perform Genome Wide Association Study. +GAPIT implements a series of methods for Genome Wide Association and Genomic Selection. +Dependencies : +Biobase (Base functions for bioconductor ) +BiocGenerics (S4 generic functions used in bioconductor) +BiocManager (Access the Bioconductor package repository) +#Swirl & Swirlify (After Packing) +curl & RCurl (Managing urls) +Install all of them before proceeding + +#Step 1 : Creating Directories & Downloading the Tutorial Data +```{r} +setwd("/Users/Public") +dir.create("GWAS_GAPIT") +setwd("/Users/Public/GWAS_GAPIT") +library("Biobase") +library("BiocGenerics") +library("BiocManager") +library("curl") +library("RCurl") +download.file(url = "http://zzlab.net/GAPIT/GAPIT_Tutorial_Data.zip", destfile="GAPIT_Tutorial_Data.zip") +unzip("GAPIT_Tutorial_Data.zip") +setwd("/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data") +``` +#Step 2 : Getting GAPIT Functions & Libraries +```{r} +source("http://zzlab.net/GAPIT/GAPIT.library.R") +source("http://zzlab.net/GAPIT/gapit_functions.txt") +source("http://www.zzlab.net/GAPIT/emma.txt") +``` +#Step 3 : Calling the Packages +```{r} +library("multtest") #Resampling-based multiple hypothesis testing +library("gplots") #Plotting Graphs +library("LDheatmap") #Graphical Display of pairwise linkage disequilibria between SNPs +library("genetics") #population genetics +library("MASS") #Support functions & datasets for venables & Ripley's MASS +library("compiler") +library("RColorBrewer") #ColourBrewer Package +library("scatterplot3d") #3D Scatterplot +``` +#Step 4 : Reading files & Calling GAPIT +```{r} +setwd("/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data") +myY <- read.table("mdp_traits.txt", head = TRUE) +myG <- read.table("mdp_genotype_test.hmp.txt", head = FALSE) +myGAPIT <- GAPIT( Y=myY,G=myG,PCA.total=3 ) +``` +/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data has the output + From 62b14549a10de00ad28ada8951398c21f2bfdcf5 Mon Sep 17 00:00:00 2001 From: Jasdeep Singh Date: Sun, 8 Nov 2020 22:10:01 +0530 Subject: [PATCH 3/4] course update --- GWAS.rmd | 50 ----------------- .../Calling_the_Packages/customTests.R | 12 +++++ .../Calling_the_Packages/dependson.txt | 0 .../Calling_the_Packages/initLesson.R | 4 ++ .../Calling_the_Packages/lesson.yaml | 11 ++++ GWAS_using_GAPIT/Data_Types/customTests.R | 12 +++++ GWAS_using_GAPIT/Data_Types/dependson.txt | 0 GWAS_using_GAPIT/Data_Types/initLesson.R | 4 ++ GWAS_using_GAPIT/Data_Types/lesson.yaml | 36 +++++++++++++ .../customTests.R | 12 +++++ .../dependson.txt | 0 .../initLesson.R | 4 ++ .../lesson.yaml | 25 +++++++++ .../customTests.R | 12 +++++ .../dependson.txt | 0 .../initLesson.R | 4 ++ .../lesson.yaml | 22 ++++++++ GWAS_using_GAPIT/Introduction/customTests.R | 12 +++++ GWAS_using_GAPIT/Introduction/dependson.txt | 0 GWAS_using_GAPIT/Introduction/initLesson.R | 4 ++ GWAS_using_GAPIT/Introduction/lesson.yaml | 20 +++++++ GWAS_using_GAPIT/MANIFEST | 7 +++ GWAS_using_GAPIT/Outputs/customTests.R | 12 +++++ GWAS_using_GAPIT/Outputs/dependson.txt | 0 GWAS_using_GAPIT/Outputs/initLesson.R | 4 ++ GWAS_using_GAPIT/Outputs/lesson.yaml | 54 +++++++++++++++++++ .../customTests.R | 12 +++++ .../dependson.txt | 0 .../initLesson.R | 4 ++ .../Reading_files_&_Calling_GAPIT/lesson.yaml | 31 +++++++++++ 30 files changed, 318 insertions(+), 50 deletions(-) delete mode 100644 GWAS.rmd create mode 100644 GWAS_using_GAPIT/Calling_the_Packages/customTests.R create mode 100644 GWAS_using_GAPIT/Calling_the_Packages/dependson.txt create mode 100644 GWAS_using_GAPIT/Calling_the_Packages/initLesson.R create mode 100644 GWAS_using_GAPIT/Calling_the_Packages/lesson.yaml create mode 100644 GWAS_using_GAPIT/Data_Types/customTests.R create mode 100644 GWAS_using_GAPIT/Data_Types/dependson.txt create mode 100644 GWAS_using_GAPIT/Data_Types/initLesson.R create mode 100644 GWAS_using_GAPIT/Data_Types/lesson.yaml create mode 100644 GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/customTests.R create mode 100644 GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/dependson.txt create mode 100644 GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/initLesson.R create mode 100644 GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/lesson.yaml create mode 100644 GWAS_using_GAPIT/Getting_the_data_&_required_packages/customTests.R create mode 100644 GWAS_using_GAPIT/Getting_the_data_&_required_packages/dependson.txt create mode 100644 GWAS_using_GAPIT/Getting_the_data_&_required_packages/initLesson.R create mode 100644 GWAS_using_GAPIT/Getting_the_data_&_required_packages/lesson.yaml create mode 100644 GWAS_using_GAPIT/Introduction/customTests.R create mode 100644 GWAS_using_GAPIT/Introduction/dependson.txt create mode 100644 GWAS_using_GAPIT/Introduction/initLesson.R create mode 100644 GWAS_using_GAPIT/Introduction/lesson.yaml create mode 100644 GWAS_using_GAPIT/MANIFEST create mode 100644 GWAS_using_GAPIT/Outputs/customTests.R create mode 100644 GWAS_using_GAPIT/Outputs/dependson.txt create mode 100644 GWAS_using_GAPIT/Outputs/initLesson.R create mode 100644 GWAS_using_GAPIT/Outputs/lesson.yaml create mode 100644 GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/customTests.R create mode 100644 GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/dependson.txt create mode 100644 GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/initLesson.R create mode 100644 GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/lesson.yaml diff --git a/GWAS.rmd b/GWAS.rmd deleted file mode 100644 index 7c4bf9e..0000000 --- a/GWAS.rmd +++ /dev/null @@ -1,50 +0,0 @@ -Using Genome Association and Prediction Integrated Tool (GAPIT) to perform Genome Wide Association Study. -GAPIT implements a series of methods for Genome Wide Association and Genomic Selection. -Dependencies : -Biobase (Base functions for bioconductor ) -BiocGenerics (S4 generic functions used in bioconductor) -BiocManager (Access the Bioconductor package repository) -#Swirl & Swirlify (After Packing) -curl & RCurl (Managing urls) -Install all of them before proceeding - -#Step 1 : Creating Directories & Downloading the Tutorial Data -```{r} -setwd("/Users/Public") -dir.create("GWAS_GAPIT") -setwd("/Users/Public/GWAS_GAPIT") -library("Biobase") -library("BiocGenerics") -library("BiocManager") -library("curl") -library("RCurl") -download.file(url = "http://zzlab.net/GAPIT/GAPIT_Tutorial_Data.zip", destfile="GAPIT_Tutorial_Data.zip") -unzip("GAPIT_Tutorial_Data.zip") -setwd("/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data") -``` -#Step 2 : Getting GAPIT Functions & Libraries -```{r} -source("http://zzlab.net/GAPIT/GAPIT.library.R") -source("http://zzlab.net/GAPIT/gapit_functions.txt") -source("http://www.zzlab.net/GAPIT/emma.txt") -``` -#Step 3 : Calling the Packages -```{r} -library("multtest") #Resampling-based multiple hypothesis testing -library("gplots") #Plotting Graphs -library("LDheatmap") #Graphical Display of pairwise linkage disequilibria between SNPs -library("genetics") #population genetics -library("MASS") #Support functions & datasets for venables & Ripley's MASS -library("compiler") -library("RColorBrewer") #ColourBrewer Package -library("scatterplot3d") #3D Scatterplot -``` -#Step 4 : Reading files & Calling GAPIT -```{r} -setwd("/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data") -myY <- read.table("mdp_traits.txt", head = TRUE) -myG <- read.table("mdp_genotype_test.hmp.txt", head = FALSE) -myGAPIT <- GAPIT( Y=myY,G=myG,PCA.total=3 ) -``` -/Users/Public/GWAS_GAPIT/GAPIT_Tutorial_Data has the output - diff --git a/GWAS_using_GAPIT/Calling_the_Packages/customTests.R b/GWAS_using_GAPIT/Calling_the_Packages/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Calling_the_Packages/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Calling_the_Packages/dependson.txt b/GWAS_using_GAPIT/Calling_the_Packages/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Calling_the_Packages/initLesson.R b/GWAS_using_GAPIT/Calling_the_Packages/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Calling_the_Packages/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Calling_the_Packages/lesson.yaml b/GWAS_using_GAPIT/Calling_the_Packages/lesson.yaml new file mode 100644 index 0000000..5669886 --- /dev/null +++ b/GWAS_using_GAPIT/Calling_the_Packages/lesson.yaml @@ -0,0 +1,11 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Calling the Packages + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + + +- Class: text + Output: Install & include multtest, gplots, LDheatmap, genetics, MASS, compiler, RColorBrewer, scatterplot3d diff --git a/GWAS_using_GAPIT/Data_Types/customTests.R b/GWAS_using_GAPIT/Data_Types/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Data_Types/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Data_Types/dependson.txt b/GWAS_using_GAPIT/Data_Types/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Data_Types/initLesson.R b/GWAS_using_GAPIT/Data_Types/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Data_Types/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Data_Types/lesson.yaml b/GWAS_using_GAPIT/Data_Types/lesson.yaml new file mode 100644 index 0000000..f7a180c --- /dev/null +++ b/GWAS_using_GAPIT/Data_Types/lesson.yaml @@ -0,0 +1,36 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Data + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: text + Output: Types of input data Phenotypic Data & Genotypic Data & Types of Output Manhattan plots + +- Class: text + Output: Phenotype data looks like + +- Class: text + Output: Genotype data can be in many formats like genotype data in hapmap format; genotype data in numerical format; genotype map; kinship; covariate variables + +- Class: text + Output: We will use hapmap format where the SNP information (chromosome and position) and genotype of each taxa to be stored in one file. + +- Class: text + Output: SNP name , the chrom column and the pos are used + +- Class: text + Output: + analysis + General Linear Model (GLM) + Mixed Linear Model (MLM) + Compressed MLM (CMLM) + Enriched CMLM (ECMLM) + Settlement of MLM Under Progressively Exclusive Relationship (SUPER) + Fixed and random model Circulating Probability Unification (FarmCPU) + Bayesian-information and Linkagedisequilibrium Iteratively Nested Keyway (BLINK) + We would not explain these models one can get inference from which they find suitable, anyhow litrature suggests BLINK > FarmCPU> MLMM > SUPER > ECMLM > CMLM > MLM > GLM. + + diff --git a/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/customTests.R b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/dependson.txt b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/initLesson.R b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/lesson.yaml b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/lesson.yaml new file mode 100644 index 0000000..4198393 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/lesson.yaml @@ -0,0 +1,25 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Getting GAPIT Functions & Libraries + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: cmd_question + Output: read this code http://zzlab.net/GAPIT/GAPIT.library.R + CorrectAnswer: source("http://zzlab.net/GAPIT/GAPIT.library.R") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: source("http://zzlab.net/GAPIT/GAPIT.library.R") + +- Class: cmd_question + Output: read this function http://zzlab.net/GAPIT/gapit_functions.txt + CorrectAnswer: source("http://zzlab.net/GAPIT/gapit_functions.txt") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: source("http://zzlab.net/GAPIT/gapit_functions.txt") + +- Class: cmd_question + Output: read this function http://www.zzlab.net/GAPIT/emma.txt for using Efficient Mixed-Model Association + CorrectAnswer: source("http://www.zzlab.net/GAPIT/emma.txt") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: source("http://www.zzlab.net/GAPIT/emma.txt") diff --git a/GWAS_using_GAPIT/Getting_the_data_&_required_packages/customTests.R b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Getting_the_data_&_required_packages/dependson.txt b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Getting_the_data_&_required_packages/initLesson.R b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Getting_the_data_&_required_packages/lesson.yaml b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/lesson.yaml new file mode 100644 index 0000000..2cb62b5 --- /dev/null +++ b/GWAS_using_GAPIT/Getting_the_data_&_required_packages/lesson.yaml @@ -0,0 +1,22 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Getting the data & required packages + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: text + Output: install Packages Biobase, BiocGenerics, BiocManager, curl & RCurl + +- Class: cmd_question + Output: download this file http://zzlab.net/GAPIT/GAPIT_Tutorial_Data.zip + CorrectAnswer: download.file(url = "http://zzlab.net/GAPIT/GAPIT_Tutorial_Data.zip", destfile="GAPIT_Tutorial_Data.zip") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: download.file(url = "http://zzlab.net/GAPIT/GAPIT_Tutorial_Data.zip", destfile="GAPIT_Tutorial_Data.zip") + +- Class: cmd_question + Output: unzip the downloaded file GAPIT_Tutorial_Data.zip + CorrectAnswer: unzip("GAPIT_Tutorial_Data.zip") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: unzip("GAPIT_Tutorial_Data.zip") diff --git a/GWAS_using_GAPIT/Introduction/customTests.R b/GWAS_using_GAPIT/Introduction/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Introduction/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Introduction/dependson.txt b/GWAS_using_GAPIT/Introduction/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Introduction/initLesson.R b/GWAS_using_GAPIT/Introduction/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Introduction/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Introduction/lesson.yaml b/GWAS_using_GAPIT/Introduction/lesson.yaml new file mode 100644 index 0000000..07df0d0 --- /dev/null +++ b/GWAS_using_GAPIT/Introduction/lesson.yaml @@ -0,0 +1,20 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Introduction + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: text + Output: This lesson is an introduction to GWAS & GAPIT + +- Class: text + Output: Genome-wide association study (GWAS) is an approach used in genetics to associate genome-wide set of genetic variants (SNPs) in different individuals with the observed phenotype. If one type of the variant is more frequent in members of the population with the observed trait, the variant is said to be associated with that trait. + +- Class: text + Output: GAPIT is Genomic Association and Prediction Integrated Tool (http://www.zzlab.net/GAPIT/) + +- Class: text + Output: It produces the distribution of marker density and decay of linkage equilibrium to inform user if the markers are dense enough. + diff --git a/GWAS_using_GAPIT/MANIFEST b/GWAS_using_GAPIT/MANIFEST new file mode 100644 index 0000000..8766b7a --- /dev/null +++ b/GWAS_using_GAPIT/MANIFEST @@ -0,0 +1,7 @@ +Introduction +Data_Types +Getting_the_data_&_required_packages +Getting_GAPIT_Functions_&_Libraries +Calling_the_Packages +Reading_files_&_Calling_GAPIT +Outputs diff --git a/GWAS_using_GAPIT/Outputs/customTests.R b/GWAS_using_GAPIT/Outputs/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Outputs/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Outputs/dependson.txt b/GWAS_using_GAPIT/Outputs/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Outputs/initLesson.R b/GWAS_using_GAPIT/Outputs/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Outputs/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Outputs/lesson.yaml b/GWAS_using_GAPIT/Outputs/lesson.yaml new file mode 100644 index 0000000..cf37862 --- /dev/null +++ b/GWAS_using_GAPIT/Outputs/lesson.yaml @@ -0,0 +1,54 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: outputs + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: text + Output: + Outputs + + Phenotype diagnosis + scatter plot + histogram + box plot + accumulative distribution + + Marker density + + Linkage Disequilibrium Decade + + Heterozygosis + + Principal Component (PC) plot + + Kinship plot + + Neighbor-Joining (NJ)-tree + + QQ-plot + + Manhattan Plot + + Compression Profile + + The Optimum Compression + + Model Selection Results + + Multiple traits or methods + + Genomic Prediction + + Distribution of BLUPs and their PEV + + Interactive plot + + + Tables + Association Table + Allelic Effects Table + + diff --git a/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/customTests.R b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/customTests.R new file mode 100644 index 0000000..1a4b852 --- /dev/null +++ b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/customTests.R @@ -0,0 +1,12 @@ +# Put custom tests in this file. + + # Uncommenting the following line of code will disable + # auto-detection of new variables and thus prevent swirl from + # executing every command twice, which can slow things down. + + # AUTO_DETECT_NEWVAR <- FALSE + + # However, this means that you should detect user-created + # variables when appropriate. The answer test, creates_new_var() + # can be used for for the purpose, but it also re-evaluates the + # expression which the user entered, so care must be taken. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/dependson.txt b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/dependson.txt new file mode 100644 index 0000000..e69de29 diff --git a/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/initLesson.R b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/initLesson.R new file mode 100644 index 0000000..65a4701 --- /dev/null +++ b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/initLesson.R @@ -0,0 +1,4 @@ +# Code placed in this file fill be executed every time the + # lesson is started. Any variables created here will show up in + # the user's working directory and thus be accessible to them + # throughout the lesson. \ No newline at end of file diff --git a/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/lesson.yaml b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/lesson.yaml new file mode 100644 index 0000000..1ad49a8 --- /dev/null +++ b/GWAS_using_GAPIT/Reading_files_&_Calling_GAPIT/lesson.yaml @@ -0,0 +1,31 @@ +- Class: meta + Course: GWAS using GAPIT + Lesson: Reading files & Calling GAPIT + Author: your name goes here + Type: Standard + Organization: your organization's name goes here + Version: 2.4.5 + +- Class: cmd_question + Output: set the working directory to the unziped file + CorrectAnswer: setwd("./GWAS_GAPIT/GAPIT_Tutorial_Data") + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: setwd("./GWAS_GAPIT/GAPIT_Tutorial_Data") + +- Class: cmd_question + Output: read the phenotypic data from file mdp_traits.txt & assign to variable myY + CorrectAnswer: myY <- read.table("mdp_traits.txt", head = TRUE) + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: myY <- read.table("mdp_traits.txt", head = TRUE) + +- Class: cmd_question + Output: read the hapmap data from file mdp_genotype_test.hmp.txt & assign to variable myG + CorrectAnswer: myG <- read.table("mdp_genotype_test.hmp.txt", head = FALSE) + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: myG <- read.table("mdp_genotype_test.hmp.txt", head = FALSE) + +- Class: cmd_question + Output: Use GAPIT on these variables & assign to variable myGAPIT , relax for a while + CorrectAnswer: myGAPIT <- GAPIT( Y=myY,G=myG,PCA.total=3 ) + AnswerTests: omnitest(correctExpr='EXPR', correctVal=VAL) + Hint: myGAPIT <- GAPIT( Y=myY,G=myG,PCA.total=3 ) From c97ddd156132a55d6b70b942dfff45e836a2216b Mon Sep 17 00:00:00 2001 From: Jasdeep Singh <55511370+singhomics@users.noreply.github.com> Date: Mon, 9 Nov 2020 02:51:51 +0530 Subject: [PATCH 4/4] Delete README.md --- README.md | 1 - 1 file changed, 1 deletion(-) delete mode 100644 README.md diff --git a/README.md b/README.md deleted file mode 100644 index e807d94..0000000 --- a/README.md +++ /dev/null @@ -1 +0,0 @@ -# Building out BiocSwirl interactive hands-on content on relevant bioinformatics tools, datasets, and pipeline