process_cnv_call: predict the inheritance state of a CNV call

In jeremymcrae/cifer: CNV Inheritance from Exome Read-Depths

Description

predict the inheritance state of a CNV call

Usage

process_cnv_call(samples, probes, child_id, mom_id, dad_id, cnv = NA)

Arguments

samples	dataframe listing sample IDs, and file paths
probes	dataframe of log-2-ratio (or adm3 score) values for all participants, for the exome probes that lie within the CNV region.
child_id	ID of the proband
mom_id	sample ID for the proband's mother
dad_id	sample ID for the proband's father
cnv	row information for CNV, include this if you want to plot the underlying data for the inheritance prediction

Value

list of inheritance classification, the mother's p-value and the father's p-value.

Examples

samples = read.table(header=TRUE, text="
       individual_id is_proband
       A             FALSE
       B             FALSE
       C             FALSE
       D             FALSE
       E             TRUE
       F             FALSE
       G             FALSE
       H             FALSE
       I             FALSE
       J             FALSE
       K             TRUE
       L             FALSE",
       colClasses=c("character", "logical"))
probes = read.table(header=TRUE, text="
       probe A B C D E F G H I J K
       p1    5 6 4 5 5 6 5 5 4 6 9
       p2    5 6 4 5 5 6 5 5 4 6 9
       p3    5 6 4 5 5 6 5 5 4 6 9
       p4    5 6 4 5 5 6 5 5 4 6 9")
child_id = "K"
mom_id = "J"
dad_id = "I"
process_cnv_call(samples, probes, child_id, mom_id, dad_id)

# run another example, this time with a larger dataset
cohort_n = 500
sample_ids = paste("sample", 1:cohort_n, sep="_")
samples = data.frame("individual_id"=sample_ids,
    "is_proband"=c(rep(FALSE, length(sample_ids) - 1), TRUE))

# define the population as having probes values cenetred around zero
probes = data.frame(matrix(rnorm(length(sample_ids) * 5), nrow=5))
names(probes) = sample_ids

# set the child probe values to distant from the population values
probes[sample_ids[length(sample_ids)]] = rnorm(5, mean=10, sd=1)

# define the sample IDs for the trio members
child_id = sample_ids[length(sample_ids)]
mom_id = sample_ids[1]
dad_id = sample_ids[2]

process_cnv_call(samples, probes, child_id, mom_id, dad_id)

jeremymcrae/cifer documentation built on May 19, 2019, 5:08 a.m.