bigsnpr (version 1.12.15)

snp_getSampleInfos: Get sample information

Description

Get information of individuals by matching from an external file.

Usage

snp_getSampleInfos(
  x,
  df.or.files,
  col.family.ID = 1,
  col.sample.ID = 2,
  col.infos = -c(1, 2),
  pair.sep = "-_-",
  ...
)

Value

The requested information as a data.frame.

Arguments

x

A bigSNP.

df.or.files

Either

• A data.frame,

• A character vector of file names where to find at the information you want. You should have one column for family IDs and one for sample IDs.

col.family.ID

Index of the column containing the family IDs to match with those of the study. Default is the first one.

col.sample.ID

Index of the column containing the sample IDs to match with those of the study. Default is the second one.

col.infos

Indices of the column containing the information you want. Default is all but the first and the second columns.

pair.sep

Separator used for concatenation of family and sample IDs to make unique IDs for matching between the two datasets. Default is "-_-".

...

Any additional parameter to pass to bigreadr::fread2(). Particularly, option header = FALSE is sometimes needed.

See Also

list.files

Examples

test <- snp_attachExtdata()
table(test$fam$family.ID)

# Get populations clusters from external files
files <- system.file("extdata", paste0("cluster", 1:3), package = "bigsnpr")
bigreadr::fread2(files[1])
bigreadr::fread2(files[1], header = FALSE)  # need header option here

infos <- snp_getSampleInfos(test, files, header = FALSE)
table(infos[[1]])