process_cnv_call: predict the inheritance state of a CNV call

Description Usage Arguments Value Examples

View source: R/process_cnv_call.R

Description

predict the inheritance state of a CNV call

Usage

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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

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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 17, 2017, 6:06 p.m.