syncheck: Identifies Base Pair Change

In corTools: Tools for processing data after a Genome Wide Association Study

Description

Checks against user-inputted data to see if the SNP causes a basepair change.

Usage

syncheck(dat, chrom, pos, col1, col2)

Arguments

dat	Dataset name of the data of chromosome number, SNP position, and base information.
chrom	Chromosome number you would like to check, corresponding to the SNP position.
pos	SNP position you would like to check, corresponding to the chromosome number.
col1	Name of the column of the dataset that holds the chromosome number information.
col2	Name of the column of the dataset that holds the SNP position information.

Details

This function requires SNP basepair change information that is normally retrieved from the web. This data can also be read into R as a dataframe, but must be read in with a header, as the column names are used as arguments for this function. The information returned from this function can be used to check if the basepair change at that SNP position leads to an amino acid change (synonymous or nonsynonymous) using TAIR and Expasy.

Value

Returns the row of the user-inputted data containing the SNP basepair information of the SNP position on the specificed chromosome.

Author(s)

Angela Fan

References

Atwell S, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465(7298):627-631.

See Also

candpull, to identify SNP positions of interest

Examples

# Create sample dataset 
chromosome <- c(1, 1, 1, 2, 5)
position <- c(1432, 1542, 6834, 4642, 6435)
bp1 <- c("A", "G", "A", "T", "C")
bp2 <- c("A", "G", "T", "T", "G")
bp3 <- c("A", "C", "A", "G", "C")
bp4 <- c("A", "G", "A", "G", "C")
bp5 <- c("C", "G", "T", "G", "G")
snplist <- cbind(chromosome, position, bp1, bp2, bp3, bp4, bp5)

syncheck(snplist, 1, 6834, chromosome, position)
# snplist is the name of the dataset
# 1 and 6834 represent user query for a SNP hit on that chromosome and at that position
# chromosome and position are the names of the dataset columns that hold the information
# of chromosome and position. 
# function returns the information that on chromosome 1, position 6834, the pattern is
# "A" "T" "A" "A" "T"

corTools documentation built on May 2, 2019, 6:39 a.m.