Genes.df.example: Gene data

Description Usage Format

Description

A dataset containing Gene data

A dataset containing Gene data

Usage

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Format

Dataframe, one row per SNP, with 6 columns

Gene

Gene symbol/name for which the Coordinate data refers to. Data type: character Note: gene symbol/name must match entries in eQTL.df to ensure proper matching.

CHR

Chromosome the gene is on. Data type: integer Note: do not include a "car" prefix, and sex chromosomes should be coded numerically.

Start

Chromosomal coordinate of start position (in basepairs) to use for gene. Data type: integer Note: this should be the smaller of the two values between Start and Stop.

Stop

Chromosomal coordinate of end position (in basepairs) to use for gene. Data type: integer Note: this should be the larger of the two values between Start and Stop.

build

The genome build (either "hg19" or "hg38") for the coordinate data. Data type: character The default Genes.df dataframe contains entries for both genome builds for each gene, and the script will select the appropriate entry based on the specified gbuild (default is hg19)).

Dataframe, one row per SNP, with 6 columns

Gene

Gene symbol/name for which the Coordinate data refers to. Data type: character Note: gene symbol/name must match entries in eQTL.df to ensure proper matching.

CHR

Chromosome the gene is on. Data type: integer Note: do not include a "car" prefix, and sex chromosomes should be coded numerically.

Start

Chromosomal coordinate of start position (in basepairs) to use for gene. Data type: integer Note: this should be the smaller of the two values between Start and Stop.

Stop

Chromosomal coordinate of end position (in basepairs) to use for gene. Data type: integer Note: this should be the larger of the two values between Start and Stop.

build

The genome build (either "hg19" or "hg38") for the coordinate data. Data type: character The default Genes.df dataframe contains entries for both genome builds for each gene, and the script will select the appropriate entry based on the specified gbuild (default is hg19).


RitchieLab/eQTpLot documentation built on April 29, 2021, 8:21 p.m.