gene annotation counts

Description

The function returns a matrix with allelic counts per gene per individual for annotated SNPs

Usage

gene_annot_counts(dt_gen,dt_snpgene,keep_indiv=NULL,
extract_SNP=NULL,filter_gene=NULL,
impute_missing=FALSE,impute_method="mean")

Arguments

Details

Inputs needed are recoded genetic data formatted in PLINK format (.raw) and SNP-gene annotation data. The first six columns of the input genetic data follow standard PLINK .raw format. Column names as FID, IID, PAT, MAT, SEX and PHENOTYPE followed by SNP information as recoded by the PLINK software. SNP-gene data has two columns: GENE and SNP names. The function returns allelic counts per gene per sample (where each row represents a gene and each column represents an individual starting with the second column where first column contains gene information).

Value

Returns an object of data.table class as an output with allelic gene counts within each sample where each row corresponds to gene and column to individual IDs from column second. The first column contains gene names.

Author(s)

Sanjeev Sariya

Examples

#Package provides sample data that are loaded with package loading. 

data(recodedgen) #PLINK raw formatted data of 10 individiduals with 10 SNPs

data(snpgene) #SNP and its respective GENE annotated. 
#Here 10 SNPs are shown annotated in five genes. 
#A SNP can be annotated in multiple genes. 

gene_annot_counts(recodedgen,snpgene) #run the function

#subset Genes
gene_annot_counts(recodedgen,snpgene,filter_gene=c("GENE1","GENE2"))

#Subset individuals
gene_annot_counts(recodedgen, snpgene,keep_indiv=c("IID_sample1","IID_sample8"))

#subset with genes and samples
gene_annot_counts(recodedgen,snpgene,filter_gene=c("GENE1","GENE2"),
keep_indiv=c("IID_sample1","IID_sample8"))

#impute missing using default method. 

gene_annot_counts(recodedgen,snpgene,impute_missing=TRUE)

#Subset on individuals and impute for missing values. Default as mean
gene_annot_counts(recodedgen,snpgene,impute_missing=TRUE,
keep_indiv=c("IID_sample1","IID_sample2","IID_sample10"))

#impute using median method
gene_annot_counts(recodedgen,snpgene,impute_missing=TRUE,impute_method="median")

#end not RUN

gene position counts

Description

Function returns matrix with allelic counts per gene per individual for SNP and gene coordinates as inputs

Usage

gene_pos_counts(dt_gen,dt_snp,dt_gene,keep_indiv=NULL,
extract_SNP=NULL,filter_gene=NULL,
impute_missing=FALSE,impute_method="mean")

Arguments

Details

Inputs needed are: recoded genetic data formatted in PLINK format, SNP name with BP (position) and gene name with START and END position. The first six columns of the input genetic data follow standard PLINK .raw format. Column names as FID, IID, PAT, MAT, SEX and PHENOTYPE followed by SNP information as recoded by the PLINK software. The function returns allelic counts per gene per sample (where each row represents a gene and each column represents an individual starting with the second column where first column contains gene information).

Value

Returns an object of data.table class as an output with allelic gene counts within each sample where each row corresponds to gene and column to individual IDs from column second. The first column contains gene names.

Author(s)

Sanjeev Sariya

Examples

#Package provides sample data that are loaded with package loading. 
#not RUN
data(recodedgen) #PLINK raw formatted data of 10 individiduals with 10 SNPs

data(genecoord) #gene coordinates with START, END, CHR and GENE names. 
#Five genes with start and end genomic coordinates

data(snppos) #SNP and BP column names with SNP names and SNP genomic location in BP. 
#10 SNPs with genomic location

gene_pos_counts(recodedgen, snppos, genecoord) #run the function

#subset individuals
gene_pos_counts(recodedgen, snppos, genecoord,keep_indiv=c("IID_sample2","IID_sample4"))

#subset genes
gene_pos_counts(recodedgen,snppos,genecoord,filter_gene=c("GENE1","GENE2")) 

#subset genes and individual iids
gene_pos_counts(recodedgen,snppos,genecoord,filter_gene=c("GENE1","GENE2"),
keep_indiv=c("IID_sample10","IID_sample4")) 

##impute by mean
gene_pos_counts(recodedgen,snppos,genecoord,impute_missing=TRUE,impute_method="mean")

#end not RUN

genecoord

Description

sample data for gene base pair boundaries

Usage

genecoord

Format

An object of class data.frame with 5 rows and 3 columns.

Details

genecoord is example data provided with the GARCOM package. It has 3 columns and 5 rows. Column names are GENE, START and END where GENE column contains gene name, START and END indicate start BP and end BP respectively.

recodedgen

Description

sample genetic data

Usage

recodedgen

Format

An object of class data.frame with 10 rows and 16 columns.

Details

recodedgen is sample genetic data provided with the GARCOM package. It has with 10 rows and 16 columns. Where the first 6 columns are FID, IID, PAT, MAT, SEX and PHENOTYPE which are inherent from the PLINK (recode) output. Columns followed by PHENOTYPE are SNP names which are suffixed with _A, or _C or _T or _G. Each SNP column may have 0, 1, 2 or NA value. Where NA represents missingness.

sample_chr21_vcf

Description

VCF data hg19 build

Usage

sample_chr21_vcf

Format

VCF sample

Details

sample_chr21_vcf is sample VCF file provided for CHR21 for of ten individuals contains 128 SNPs

snpgene

Description

sample SNP-gene annotation data

Usage

snpgene

Format

An object of class data.frame with 10 rows and 2 columns.

Details

snpgene is sample SNP-Gene annotation data provided with the GARCOM package. It has 10 rows and 2 columns. Column names are GENE and SNP, where GENE column contains GENE names and SNP column contains SNP name that is annotated with the GENE

snppos

Description

sample data for SNP coordinates

Usage

snppos

Format

An object of class data.frame with 10 rows and 2 columns.

Details

snppos is sample SNP-BP data provided with the GARCOM package. It has 2 columns and 10 rows. Column names are SNP and BP. where SNP columns contains SNP names BP column contains position of the SNP

VCF gene position counts

Description

Function returns a matrix with allelic counts per gene per individual for SNP and gene coordinates as inputs

Usage

vcf_counts_SNP_genecoords(
  vcf_data,
  df_snppos,
  df_genecoords,
  keep_indiv = NULL,
  extract_SNP = NULL,
  filter_gene = NULL
)

Arguments

Value

Returns an matrix of data.table class as an output with allelic (reference) gene counts within each sample where each row corresponds to gene and column to individual IDs from column second. The first column contains gene names.

Author(s)

Sanjeev Sariya

Examples

## Not run: 
vcf_counts_SNP_genecoords(vcf_data_test,df_snppos_test,df_genecoords_test)

## End(Not run)

gene annotation counts using VCF data

Description

Function returns a matrix with allelic (reference) counts per gene per individual for SNP-gene annotation

Usage

vcf_counts_annot(
  vcf_data,
  df_snpgene,
  keep_indiv = NULL,
  extract_SNP = NULL,
  filter_gene = NULL
)

Arguments

Details

Inputs needed are a vcf data and a data frame of SNP-gene annotation. The function returns a matrix of allelic counts (reference) per gene per sample (where each row represents a gene and each column represents an individual starting with the second column where first column contains gene information).

Value

Returns an matrix of data.table class as an output with allelic (reference) gene counts within each sample where each row corresponds to gene and column to individual IDs from column second. The first column contains gene names.

Author(s)

Sanjeev Sariya

Examples

## Not run: 
vcf_counts_annot(vcf,df_snpgene_test)

## End(Not run)