get_annotations: Create a Table of Annotated Top SNPs for Phaseolus vulgaris

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

Description

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

Usage

get_annotations(
  df,
  type = c("bigsnp", "gapit", "mash", "rqtl2", "table"),
  n = 10,
  FDRalpha = NA,
  rangevector = c(0, 10000),
  markers = NULL,
  anno_info = NULL,
  txdb = NULL
)

Arguments

df	a data frame or tbl_df. Can be bigsnpr output, mashr output (loaded into R), gapit or r/qtl2 output (specify the path to a saved .csv file), or, for Phaseolus vulgaris intervals in another format, a data frame containing columns 'CHR', 'start', and 'end'.
type	Type of Phaseolus vulgaris genomic marker input specified by the df parameter. Options are "bigsnp", "gapit", "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.
markers	For data frames of type "mash" or "bigsnp", the same set of markers (with CHR and POS columns) as your df object.
anno_info	Gene information from Pvulgaris_442_v2.1.annotation_info.txt
txdb	Annotation information from Pvulgaris_442_v2.1.gene.txdb.sqlite

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.

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.