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Create list with phenotypes in region

pheno_region.Rd

Create list with phenotypes in region

Create list with expression phenotypes in region

Usage

pheno_region(
  chr_id,
  scan_window,
  covar,
  map,
  peaks_df,
  pheno_data,
  drivers = 2
)

expr_region(
  chr_id,
  scan_window,
  covar,
  map,
  project_dir,
  drivers = 2,
  query_mrna = create_mrna_query_func(project_dir)
)

Arguments

chr_id, scan_window

chromosome and start and end value

covar

covariate data frame

map

list or vector of map positions

peaks_df

table of peaks

pheno_data

matrix of phenotype data

drivers

number of drivers (1 or 2; default is 2)

project_dir

project directory with mRNA data in subdirector RNAseq

query_mrna

query routine for mRNA data (see create_mrna_query_func)

Value

list containing pheno, annot and covar.

See also

create_mrna_query_func

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- qtl2::read_cross2(file.path(dirpath, "DOex.zip"))
DOex <- subset(DOex, chr = "2")

# Calculate genotype and allele probabilities
pr <- qtl2::calc_genoprob(DOex, error_prob=0.002)

# Summary of coefficients at scan peak
scan_pr <- qtl2::scan1(pr, DOex$pheno)
peaks_df <- summary(scan_pr, DOex$pmap)

# Select Sex and Cohort columns of covariates
analyses_tbl <- data.frame(pheno = "OF_immobile_pct", Sex = TRUE, Cohort = TRUE)

# Get phenos in region.
out <- pheno_region("2", c(90, 100), DOex$covar, DOex$pmap, peaks_df, analyses_tbl, DOex$pheno)
#> Error in dplyr::group_by(peaks_df, .data$phenotype): Must group by variables found in `.data`.
#> ✖ Column `phenotype` is not found.
str(out)
#> Error: object 'out' not found