countRead: Count reads per sample and per marker.

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Count reads per sample and per marker.

Description

This function calculates several summary statistics of read counts per marker and per sample. Those values will be stored in the SnpAnnotaionDataFrame slot and the sample slot and obtained via getter functions, e.g. getCountReadRef() and getCountReadAlt(). This function first calculates normalized allele read counts by dividing allele read counts at each marker in each sample by the total allele read of the sample followed by multiplication by 10^6. In other words, it calculates reads per million (rpm). Then, the function calculates mean, standard deviation, quantile values of rpm per marker and per sample. The results will be stored in the SnpAnnotaionDataFrame slot and the sample slot and obtained via getter functions, e.g. getMeanReadRef() and getMedianReadAlt().

Usage

countRead(object, target = "both", node = "raw", ...)

## S4 method for signature 'GbsrGenotypeData'
countRead(object, target, node)

Arguments

object	A GbsrGenotypeData object.
target	Either of "marker" and "sample".
node	Either of "raw" and "filt". See details.
...	Unused.

Details

Read count data can be obtained from the "annotation/format/AD/data" node or the "annotation/format/AD/filt.data" node of the GDS file with node = "raw" or node = "filt", respectively. The setCallFilter() function generate filtered read count data in the "annotation/format/AD/filt.data" node which can be accessed as mentioned above.

Value

A GbsrGenotypeData object with read count information.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

# Summarize the read count information and store them in the
# [marker] and [sample] slots of the [GbsrGenotypeData] object.
gds <- countRead(gds)

# Get the total read counts per marker
read_depth_per_marker <- getCountRead(gds, target = "marker")

# Get the proportion of reference allele rads per marker.
reference_read_freq <- getCountReadRef(gds, target = "marker", prop = TRUE)

# Draw histgrams of reference allele read counts per sample and marker.
histGBSR(gds, stats = "ad_ref")

# Close the connection to the GDS file.
closeGDS(gds)

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.