GWAS GAPIT Course Merge

GWAS_using_GAPIT/Calling_the_Packages/customTests.R

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+# 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.

GWAS_using_GAPIT/Calling_the_Packages/initLesson.R

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+# 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.

GWAS_using_GAPIT/Calling_the_Packages/lesson.yaml

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+- 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

GWAS_using_GAPIT/Data_Types/customTests.R

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+# 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.

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.

GWAS_using_GAPIT/Data_Types/lesson.yaml

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+- 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.
+
+

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.

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.

GWAS_using_GAPIT/Getting_GAPIT_Functions_&_Libraries/lesson.yaml

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+- 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")

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.

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.

GWAS_using_GAPIT/Getting_the_data_&_required_packages/lesson.yaml

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+- 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")

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.

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.

GWAS_using_GAPIT/Introduction/lesson.yaml

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+- 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.
+

GWAS_using_GAPIT/MANIFEST

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+Introduction
+Data_Types
+Getting_the_data_&_required_packages
+Getting_GAPIT_Functions_&_Libraries
+Calling_the_Packages
+Reading_files_&_Calling_GAPIT
+Outputs

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.

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.

GWAS_using_GAPIT/Outputs/lesson.yaml

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+- 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
+
+

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.

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.

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 )