Create a Table of Annotated Top SNPs for Panicum virgatum — pvdiv_table

Loads in one set of GWAS results from a bigsnp GWAS, a mash object, RQTL2 output, or a dataframe with 'CHR', 'start', and 'end' columns for the genome of Panicum virgatum. Then, it constructs SNP tables meeting different criteria using these genomic intervals.

pvdiv_table_topsnps(
  df,
  type = c("bigsnp", "mash", "rqtl2", "table"),
  n = 10,
  FDRalpha = 0.1,
  rangevector = c(0, 10000),
  snp = NULL,
  txdb = NULL,
  anno_info = switchgrassGWAS::anno_info
)

Arguments

df: a data frame or tbl_df. Can be bigsnpr output, mashr output (loaded into R), r/qtl2 output (specify the path to a saved .csv file), or, for Panicum virgatum intervals in another format, a data frame containing columns 'CHR', 'start', and 'end'.
type: Type of Panicum virgatum genomic marker input specified by the df parameter. Options are "bigsnp", "mash", "rqtl2", and "table". Defaults to 'bigsnp'.
n: An integer or integer vector The numberof most significant SNPs to select (by p-value). Set to NA to omit this table. Default is 10.
FDRalpha: The false discovery rate. Numeric, a number or vector of numbers between 0 and 1. Set to NA to omit this table. Default is 0.1.
rangevector: How far from the significant SNP should annotations be pulled? Can be an integer or a vector of integers. Default is 0 (the SNP itself) and a 10 kbp window around the SNP.
snp: For data frames of type "mash" or "bigsnp", the bigSNP object used to create your data. Load into R with bigsnpr::snp_attach().
txdb: Annotation information from Pvirgatum_516_v5.1.gene.txdb.sqlite
anno_info: Gene information from Pvirgatum_516_v5.1.annotation_info.txt

Value

A list containing dataframes of SNPs. If more than one dataframe is returned, they are named using the criteria used to select the SNPs in the dataframe.