Package 'qtl2cl'

Read cross and save as rds

Description

Read cross files and save as rds

Usage

cross2rds(input_file, output_file, compress = FALSE)

Arguments

input_file	Character string with path to the YAML or JSON file containing all of the control information. This could instead be a zip file containing all of the data files, in which case the contents are unzipped to a temporary directory and then read.
output_file	Character string with path to RDS file for output
compress	If TRUE, save a compressed RDS file (smaller but slower).

Examples

input_file <- paste0("https://github.com/rqtl/qtl2data/",
                     "blob/master/B6BTBR/b6btbr.zip")
## Not run: cross2rds(input_file, "b6btbr.rds")

---

Read a file

Description

Read a file that is either RDS, CSV, JSON, or YAML, with the method determined by the file extension.

Usage

read_file(file, ...)

Arguments

file	Character string of input file; must have file extension .rds, .csv, .json, or .yaml.
...	Passed to whatever function it calls

Details

For CSV files, we use qtl2::fread_csv(), which calls data.table::fread() with a particular set of options; note that columns are forced to be numeric in this case. For RDS files, we use base::readRDS(). For JSON files, we use base::readLines() and jsonlite::fromJSON(). For YAML files, we use yaml::yaml.load_file().

Value

Could be most anything; whatever gets read in by the corresponding R function for the file type. See Details.

Examples

## Not run: w <- read_file("myfile.rds")
x <- read_file("myfile.csv")
y <- read_file("myfile.json")
z <- read_file("myfile.yaml")
## End(Not run)

---

Run calc_genoprob and save result to rds

Description

Run calc_genoprob and save result to rds

Usage

run_calcgenoprob(
  cross_file,
  output_file,
  map_file = NULL,
  step = 0,
  off_end = 0,
  stepwidth = c("fixed", "max"),
  error_prob = 0.0001,
  map_function = c("haldane", "kosambi", "c-f", "morgan"),
  cores = 1,
  compress = FALSE
)

Arguments

cross_file	Character string with path to RDS file containing cross
output_file	Character string with path to RDS file for output
map_file	Character string with path to RDS file for writing genetic map (with inserted pseudomarkers)
step	Distance between pseudomarkers and markers; if step=0 no pseudomarkers are inserted.
off_end	Distance beyond terminal markers in which to insert pseudomarkers.
stepwidth	Indicates whether to use a fixed grid (stepwidth="fixed") or to use the maximal distance between pseudomarkers to ensure that no two adjacent markers/pseudomarkers are more than step apart.
error_prob	Assumed genotyping error probability
map_function	Character string indicating the map function to use to convert genetic distances to recombination fractions.
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().
compress	If TRUE, save compressed RDS files (smaller but slower).

Examples

input_file <- paste0("https://github.com/rqtl/qtl2data/",
                     "blob/master/B6BTBR/b6btbr.zip")
## Not run: cross2rds(input_file, "b6btbr.rds")
## Not run: run_calcgenoprob("b6btbr.rds", "b6btbr_probs.rds", "b6btbr_gmap.rds")

---

Calculate kinship matrix

Description

Calculate genetic similarity among individuals (kinship matrix) from conditional genotype probabilities.

Usage

run_calckinship(
  input_file,
  output_file,
  type = c("overall", "loco", "chr"),
  omit_x = FALSE,
  use_allele_probs = TRUE,
  cores = 1,
  compress = FALSE
)

Arguments

input_file	Input RDS file containing genotype or allele probabilities
output_file	Output RDS file for calculated kinship matrix
type	Indicates whether to calculate the overall kinship ("overall", using all chromosomes), the kinship matrix leaving out one chromosome at a time ("loco"), or the kinship matrix for each chromosome ("chr").
omit_x	If TRUE, only use the autosomes; ignored when type="chr".
use_allele_probs	If TRUE, assess similarity with allele probabilities (that is, first run qtl2::genoprob_to_alleleprob()); otherwise use the genotype probabilities.
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().
compress	If TRUE, save a compressed RDS file (smaller but slower).

Examples

input_file <- paste0("https://github.com/rqtl/qtl2data/",
                     "blob/master/B6BTBR/b6btbr.zip")
## Not run: cross2rds(input_file, "b6btbr.rds")
## Not run: run_calcgenoprob("b6btbr.rds", "b6btbr_probs.rds")
## Not run: run_calckinship("b6btbr_probs.rds", "b6btbr_kinship.rds")

---

Get X covariates and write to file

Description

Read cross from RDS file, determine X chromosome covariates, and write to another RDS file.

Usage

run_getXcovar(input_file, output_file, compress = FALSE)

Arguments

input_file	Input RDS file for cross
output_file	Output RDS file for X chromosome covariates
compress	If TRUE, save a compressed RDS file (smaller but slower).

Examples

input_file <- paste0("https://github.com/rqtl/qtl2data/",
                     "blob/master/B6BTBR/b6btbr.zip")
## Not run: cross2rds(input_file, "b6btbr.rds")
## Not run: run_getXcovar("b6btbr.rds", "b6btbr_xcovar.rds")

---

Run genoprob_to_alleleprob

Description

Read in genotype probabilities, convert them to allele probabilities, and write them back out.

Usage

run_gp2ap(input_file, output_file, cores = 1, compress = FALSE)

Arguments

input_file	Name of input file (should be RDS)
output_file	Name of output file (will be RDS)
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().
compress	If TRUE, save a compressed RDS file (smaller but slower).

Examples

input_file <- paste0("https://github.com/rqtl/qtl2data/",
                     "blob/master/B6BTBR/b6btbr.zip")
## Not run: cross2rds(input_file, "b6btbr.rds")
## Not run: run_calcgenoprob("b6btbr.rds", "b6btbr_probs.rds")
## Not run: run_gp2ap("b6btbr_probs.rds", "b6btbr_aprobs.rds")

---

Run scan1

Description

Read in a bunch of data and then run qtl2::scan1().

Usage

run_scan1(
  genoprobs_file,
  pheno_file,
  output_file = NULL,
  map_file = NULL,
  kinship_file = NULL,
  addcovar_file = NULL,
  Xcovar_file = NULL,
  intcovar_file = NULL,
  weights_file = NULL,
  reml = TRUE,
  cores = 1,
  compress = FALSE
)

Arguments

genoprobs_file	Name of file with genotype probabilities
pheno_file	Name of file with phenotypes
output_file	Optional output RDS file. If NULL, print output as a table.
map_file	Optional (RDS) file containing map. Needed if output_file is NULL.
kinship_file	Optional file containing kinship matrix
addcovar_file	Optional file containing additive covariates
Xcovar_file	Optional file containing X chromosome covariates
intcovar_file	Optional file containing interactive covariates
weights_file	Optional file containing covariates
reml	If TRUE, use REML; otherwise, use maximum likelihood
cores	Number of CPU cores to use
compress	If TRUE, save a compressed RDS file (smaller but slower).

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