Merge pull request #56 from GregFa/main

added function description for new subset functions

src/io/export_to_type.jl

@@ -6,7 +6,7 @@ Creates a `Gmap` type/struct from gmap CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the gmap CSV file.
+* `filename` : A string containing the name(with directory) of the gmap CSV file.
 
 # Output
 
@@ -56,7 +56,7 @@ Creates a `CrossType` type/struct from  control file in json format.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 
@@ -85,7 +85,7 @@ Creates a `Alleles` type/struct from  control file in json format.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 
@@ -112,7 +112,7 @@ Creates a `GenoType` type/struct from  control file in json format.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 
@@ -144,7 +144,7 @@ Creates a `GenoTranspose` type/struct from  control file in json format.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 
@@ -175,7 +175,7 @@ Creates a `Geno` type/struct from gmap CSV file and geno CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 
 # Output
@@ -289,7 +289,7 @@ Creates a `Pmap` type/struct from Pmap CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the pmap CSV file.
+* `filename` : A string containing the name(with directory) of the pmap CSV file.
 
 # Output
 
@@ -354,7 +354,7 @@ Creates a `Pheno` type/struct from Pheno CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the pheno CSV file.
+* `filename` : A string containing the name(with directory) of the pheno CSV file.
 
 # Output
 
@@ -399,7 +399,7 @@ Creates a `Phenocovar` type/struct from phenocovar CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the phenocovar CSV file.
+* `filename` : A string containing the name(with directory) of the phenocovar CSV file.
 
 # Output
 
@@ -439,7 +439,7 @@ Creates a `Crossinfo` type/struct from crossinfo CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the crossinfo CSV file.
+* `filename` : A string containing the name(with directory) of the crossinfo CSV file.
 
 # Output
 
@@ -480,7 +480,7 @@ Creates a `IsXChar` type/struct from gmap CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the gmap CSV file.
+* `filename` : A string containing the name(with directory) of the gmap CSV file.
 
 # Output
 
@@ -510,7 +510,7 @@ Creates a `Covar` type/struct from gmap CSV file.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the gmap CSV file.
+* `filename` : A string containing the name(with directory) of the gmap CSV file.
 
 # Output
 
@@ -554,7 +554,7 @@ If control file does not stipulate sex information, we assume all female
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 
@@ -601,7 +601,7 @@ Creates a `GeneticStudyData` type/struct from  control file in json format.
 
 # Argument
 
-- `filename` : A string containing the name(with directory) of the control file in json format.
+* `filename` : A string containing the name(with directory) of the control file in json format.
 
 # Output
 

src/io/io_helpers.jl

@@ -5,7 +5,7 @@ Parses a JSON file to a dictionary with keys containing the names of CSV file fo
 
 # Argument
 
-- `file` : A string containing the name of the JSON file
+* `file` : A string containing the name of the JSON file
 
 # Output
 
@@ -26,7 +26,7 @@ Writes a CSV file to data frame excluding the comments lines.
 
 # Argument
 
-- `filename` : A string containing the name of the CSVfile
+* `filename` : A string containing the name of the CSVfile
 
 # Output
 
@@ -51,10 +51,10 @@ end
 Locate the control file and determine the directory where it resides.
 
 # Arguments
-- `filename::String`: A string representing either the path to a file or a directory.
+* `filename::String`: A string representing either the path to a file or a directory.
 
 # Returns
-- `(String, String)`: A tuple containing the directory of the control file and the path 
+* `(String, String)`: A tuple containing the directory of the control file and the path 
 to the control file. If the provided `filename` is a directory, the function will search 
 for JSON files within and return the path to the first JSON file found.
 
@@ -88,11 +88,11 @@ end
 Encode a matrix of genotype values using a dictionary of predefined mappings.
 
 # Arguments
-- `geno_dict::Dict{String, Any}`: A dictionary mapping genotype strings to integer codes.
-- `geno_val::AbstractArray`: An array of genotype strings to be encoded.
+* `geno_dict::Dict{String, Any}`: A dictionary mapping genotype strings to integer codes.
+* `geno_val::AbstractArray`: An array of genotype strings to be encoded.
 
 # Returns
-- `Matrix{Union{Missing, Int64}}` or `Matrix{Int64}`: A matrix of the same dimensions as 
+* `Matrix{Union{Missing, Int64}}` or `Matrix{Int64}`: A matrix of the same dimensions as 
 `geno_val` where each genotype string is replaced by its corresponding integer code. 
 Genotypes not found in `geno_dict` are encoded as `missing`.
 
@@ -156,11 +156,11 @@ end
 Check if a specified key exists in the given dictionary and return its corresponding value.
 
 # Arguments
-- `control_dict::Dict`: A dictionary from which the value associated with a key is to be retrieved.
-- `s::String`: The key for which the existence and value are checked within the dictionary.
+* `control_dict::Dict`: A dictionary from which the value associated with a key is to be retrieved.
+* `s::String`: The key for which the existence and value are checked within the dictionary.
 
 # Returns
-- `Any`: Returns the value associated with the key `s` in `control_dict` if it exists.
+* `Any`: Returns the value associated with the key `s` in `control_dict` if it exists.
 
 # Throws
 - Throws an error if the key `s` is not found in `control_dict`.
@@ -177,7 +177,7 @@ function check_key(control_dict::Dict, s::String)
 	if (in(s, keys(control_dict)))
 		val = control_dict[s]
 	else
-		@warn "Error: $(s) not found in control file"
+		@warn "$(s) file not found in control file"
 		val = missing
 		# throw("Error: $(s) not found in control file")
 	end

src/kinship/kinship.jl

@@ -10,7 +10,7 @@ Calculate kinship from the genotype probability array.
 
 # Arguments
 
-- `geno` is the genotype probability matrix for n individuals and p markers. 
+* `geno` is the genotype probability matrix for n individuals and p markers. 
 
 # Output
 
@@ -24,7 +24,7 @@ Calculate kinship from the genotype probability array.
 
 # Arguments
 
-- `geno` is the genotype probability matrix, n individuals and p markers, which 
+* `geno` is the genotype probability matrix, n individuals and p markers, which 
     contains `missing` values.
 
 # Output

src/kinship/kinship_4way.jl

@@ -10,7 +10,7 @@ Note: In [R/qtl](https://cran.r-project.org/web/packages/qtl/qtl.pdf), genotypes
 
 # Argument
 
-- `genmat` : A matrix of genotypes for `four-way cross` ``(1,2, \\dots)``.
+* `genmat` : A matrix of genotypes for `four-way cross` ``(1,2, \\dots)``.
            size(genematrix)= (p,n), for `p` genetic markers x `n` individuals(or lines).
 
 # Output

src/kinship/kinship_ctr.jl

@@ -6,7 +6,7 @@ Calculates a kinship by a centered genotype matrix (linear kernel), i.e. genotyp
 
 # Argument
 
-- `genmat` : A matrix of genotype data (0,1,2). size(genmat)=(n,p) for `n` individuals x `p` markers
+* `genmat` : A matrix of genotype data (0,1,2). size(genmat)=(n,p) for `n` individuals x `p` markers
 
 # Output
 

src/kinship/kinship_gs.jl

@@ -6,9 +6,9 @@ Computes a kinship matrix using the Gaussian Kernel.
 
 # Arguments
 
-- `climate`: A matrix of genotype or climate information data. size(climate)=(m,r), such that `r` genotype markers (or days/years of climate factors,
+* `climate`: A matrix of genotype or climate information data. size(climate)=(m,r), such that `r` genotype markers (or days/years of climate factors,
             i.e. precipitations, temperatures, etc.), and `m` individuals (or environments/sites)
-- `ρ`: A free parameter determining the width of the kernel. It could be attained empirically.
+* `ρ`: A free parameter determining the width of the kernel. It could be attained empirically.
 
 # Output
 

src/kinship/kinship_lin.jl

@@ -6,9 +6,9 @@ Calculates a kinship (or climatic relatedness, [`kinship_gs`](@ref)) matrix by l
 
 # Arguments
 
-- `mat` : A matrix of genotype (or allele) probabilities usually extracted from [R/qtl](https://rqtl.org/tutorials/rqtltour.pdf),
+* `mat` : A matrix of genotype (or allele) probabilities usually extracted from [R/qtl](https://rqtl.org/tutorials/rqtltour.pdf),
         [R/qtl2](https://kbroman.org/qtl2/assets/vignettes/user_guide.html) or the counterpart packages. size(mat)= (p,n) for p genetic markers x n individuals.
-- `cross` : A scalar indicating instances of alleles or genotypes in a genetic marker. ex. 1 for genotypes (labeled as 0,1,2), 2 for RIF, 4 for four-way cross, 8 for HS mouse (allele probabilities), etc.
+* `cross` : A scalar indicating instances of alleles or genotypes in a genetic marker. ex. 1 for genotypes (labeled as 0,1,2), 2 for RIF, 4 for four-way cross, 8 for HS mouse (allele probabilities), etc.
 
 # Output
 

src/kinship/kinship_man.jl

@@ -7,7 +7,7 @@ This function is for recombinant inbred line (RIL) (AA/BB), not for 4-way cross-
 
 # Argument
 
-- `genematrix` : A matrix of genotypes, i.e. 0,1 (or 1,2).  size(genematrix)= (p,n) for `p` genetic markers x `n` individuals(or lines).
+* `genematrix` : A matrix of genotypes, i.e. 0,1 (or 1,2).  size(genematrix)= (p,n) for `p` genetic markers x `n` individuals(or lines).
 
 
 # Output

src/kinship/kinship_std.jl

@@ -8,7 +8,7 @@ It can also do with climatic information data. See [`kinship_gs`](@ref).
 
 # Argument
 
-- `genmat` : A matrix of genotype data (0,1,2). size(genmat)=(n,p) for `n` individuals x `p` markers
+* `genmat` : A matrix of genotype data (0,1,2). size(genmat)=(n,p) for `n` individuals x `p` markers
 
 # Output
 

src/kinship/shrinkg.jl

@@ -7,9 +7,9 @@ This function runs faster by CPU parallelization.  Add workers/processes using `
 
 # Arguments
 
-- `f `: A function of computing a kinship. It can only be used with [`kinship_man`](@ref), [`kinship_4way`](@ref).
-- `nb` : An integer indicating the number of bootstraps. It does not have to be a large number.
-- `geno` : A matrix of genotypes. See [`kinship_man`](@ref), [`kinship_4way`](@ref) for dimension.
+* `f `: A function of computing a kinship. It can only be used with [`kinship_man`](@ref), [`kinship_4way`](@ref).
+* `nb` : An integer indicating the number of bootstraps. It does not have to be a large number.
+* `geno` : A matrix of genotypes. See [`kinship_man`](@ref), [`kinship_4way`](@ref) for dimension.
 
 # Example
 

src/loco/loco_bulkscan.jl

@@ -5,9 +5,9 @@ Single trait scan without covariates for LOCO data structure.
 
 # Arguments
 
-- `y`is the phenotype column matrix. 
-- `dfG`is is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
-- `kwargs` are optional keywords arguments pertaining to the `BulkLMM.bulkscan()` function. For
+* `y`is the phenotype column matrix. 
+* `dfG`is is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
+* `kwargs` are optional keywords arguments pertaining to the `BulkLMM.bulkscan()` function. For
 	example: 
 	- method::String = "null-grid", h2_grid::Array{Float64, 1} = collect(0.0:0.1:0.9),
 	- nb::Int64 = Threads.nthreads(), 
@@ -34,10 +34,10 @@ Single trait scan without covariates for LOCO data structure.
 
 # Arguments
 
-- `y`is the phenotype column matrix. 
-- `G`is vector of genotype matrices based on the chromosome.
-- `K` is a vector of kinship matrices.
-- `kwargs` are optional keywords arguments pertaining to the `BulkLMM.scan()` function. For
+* `y`is the phenotype column matrix. 
+* `G`is vector of genotype matrices based on the chromosome.
+* `K` is a vector of kinship matrices.
+* `kwargs` are optional keywords arguments pertaining to the `BulkLMM.scan()` function. For
 	example: 
 	- method::String = "null-grid", h2_grid::Array{Float64, 1} = collect(0.0:0.1:0.9),
 	- nb::Int64 = Threads.nthreads(), 
@@ -63,11 +63,11 @@ Single trait scan with covariates for LOCO data structure.
 
 # Arguments
 
-- `y`is the phenotype column matrix. 
-- `G`is vector of genotype matrices based on the chromosome.
-- `covar` is covariate column matrix.
-- `K` is a vector of kinship matrices.
-- `kwargs` are optional keywords arguments pertaining to the `BulkLMM.scan()` function. For
+* `y`is the phenotype column matrix. 
+* `G`is vector of genotype matrices based on the chromosome.
+* `covar` is covariate column matrix.
+* `K` is a vector of kinship matrices.
+* `kwargs` are optional keywords arguments pertaining to the `BulkLMM.scan()` function. For
 	example: 
 	- method::String = "null-grid", h2_grid::Array{Float64, 1} = collect(0.0:0.1:0.9),
 	- nb::Int64 = Threads.nthreads(), 

src/loco/loco_helpers.jl

@@ -4,9 +4,9 @@ get_loco_geno(dfG::DataFrame; chromosome_colname::String = "Chr", idx_start::Int
 Returns a vector of genotype matrices based on the chromosome.
 
 # Arguments
-- `dfG` is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
-- `chromosome_colname` column name containing chromosome information
-- `idx_start` indicates the first column index containing the genotype values 
+* `dfG` is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
+* `chromosome_colname` column name containing chromosome information
+* `idx_start` indicates the first column index containing the genotype values 
 """
 function get_loco_geno(dfG::DataFrame;
 	chromosome_colname::String = "Chr",
@@ -34,9 +34,9 @@ get_loco_geno_info(dfG::DataFrame; chromosome_colname::String = "Chr", idx_info
 Returns a vector of genotype information dataframes based on the chromosome.
 
 # Arguments
-- `dfG` is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
-- `chromosome_colname` column name containing chromosome information
-- `idx_info` indicates columns containing genotype information (e.g., Locus, Mb...) 
+* `dfG` is a dataframe containing genotype values and genotype info such as the chromosome, loci... 
+* `chromosome_colname` column name containing chromosome information
+* `idx_info` indicates columns containing genotype information (e.g., Locus, Mb...) 
 """
 function get_loco_geno_info(dfG::DataFrame;
 	chromosome_colname = "Chr",
@@ -57,7 +57,7 @@ Calculates kinship matrices leaving out one chromosome out, and returns a vector
 of kinship matrices per chromosome.
 
 # Arguments
-- `G` is a vector of genotype matrices
+* `G` is a vector of genotype matrices
 """
 function calcLocoKinship(G::Vector{Matrix{Float64}})