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REFERENCE.SAMPLE.SET.SELECTOR package (#64)
* init REFERENCE.SAMPLE.SET.SELECTOR package * function for selecting reference sample set from CANOES cnv caller * function for selecting reference sample set from ExomeDepth cnv caller * select reference set sdded to EXOMEDEPTHCOV package * bugfix and add fields to parameters sql model
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| @@ -1,24 +1,16 @@ | ||
| library('CODEXCOV') | ||
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| #' Function Description | ||
| #' | ||
| #' Function description. | ||
| #' @param K_from | ||
| #' @param K_to | ||
| #' @param lmax | ||
| #' @param cov_table | ||
| #' @keywords | ||
| #' @export | ||
| #' @examples | ||
| #' run_wrapper_CODEXCOV | ||
| run_wrapper_CODEXCOV <- function(K_from, | ||
| K_to, | ||
| lmax, | ||
| reference_set_select_method, | ||
| num_of_samples_in_reference_set, | ||
| cov_table){ | ||
| calls <- run_CODEXCOV(strtoi(K_from), | ||
| strtoi(K_to), | ||
| strtoi(lmax), | ||
| cov_table | ||
| ) | ||
| reference_set_select_method, | ||
| strtoi(num_of_samples_in_reference_set), | ||
| cov_table) | ||
| calls | ||
| } |
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| @@ -1,7 +1,10 @@ | ||
| library('EXOMEDEPTHCOV') | ||
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| run_wrapper_EXOMEDEPTHCOV <- function(cov_table){ | ||
| calls <- run_EXOMEDEPTHCOV(cov_table | ||
| ) | ||
| run_wrapper_EXOMEDEPTHCOV <- function(reference_set_select_method, | ||
| num_of_samples_in_reference_set, | ||
| cov_table){ | ||
| calls <- run_EXOMEDEPTHCOV(reference_set_select_method, | ||
| num_of_samples_in_reference_set, | ||
| cov_table) | ||
| calls | ||
| } |
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| Package: REFERENCE.SAMPLE.SET.SELECTOR | ||
| Title: Package For Selecting Reference Sample Set | ||
| Version: 0.0.1 | ||
| Authors@R: c( | ||
| person("Tomasz", "Gambin", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Marek", "Wiewiórka", email = "[email protected]", role = c("aut")), | ||
| person("Wiktor", "Kuśmirek", email = "[email protected]", role = c("aut"))) | ||
| Description: An implementation of the package with multiple function | ||
| for selecting reference sample set. | ||
| Depends: | ||
| R (>= 3.2.3), | ||
| ExomeDepth (>= 1.1.10) | ||
| License: GPL-3 | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 6.0.1.9000 |
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| # Generated by roxygen2: fake comment so roxygen2 overwrites silently. | ||
| exportPattern("^[^\\.]") |
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R/REFERENCE.SAMPLE.SET.SELECTOR/R/functions_REFERENCE.SAMPLE.SET.SELECTOR.R
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| library(ExomeDepth) | ||
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| canoes_method <- function(investigated_sample, Y, num_refs){ | ||
| if (num_refs == 0) { | ||
| num_refs <- 30 # in CANOES application num_refs is default set to 30 | ||
| } | ||
| samples <- colnames(Y) | ||
| cov <- cor(Y[, samples], Y[, samples]) | ||
| reference_samples <- setdiff(samples, investigated_sample) | ||
| covariances <- cov[investigated_sample, reference_samples] | ||
| reference_samples <- names(sort(covariances, | ||
| decreasing=T)[1:min(num_refs, length(covariances))]) | ||
| return(list(reference_samples=reference_samples)) | ||
| } | ||
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| exomedepth_method <- function(investigated_sample, Y, num_refs, target_length){ | ||
| samples <- colnames(Y) | ||
| reference_samples <- setdiff(samples, investigated_sample) | ||
| reference_set <- select.reference.set(test.counts = Y[,investigated_sample], | ||
| reference.counts = Y[,reference_samples], | ||
| bin.length = target_length, | ||
| n.bins.reduced = 10000) | ||
| if (num_refs == 0) { | ||
| reference_samples <- reference_set$reference.choice | ||
| } else { | ||
| reference <- reference_set$summary.stats[1:num_refs,'ref.samples'] | ||
| reference_samples <- c() | ||
| for (s in reference) | ||
| reference_samples <- c(reference_samples, c(s)) | ||
| } | ||
| return(list(reference_samples=reference_samples)) | ||
| } |
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R/REFERENCE.SAMPLE.SET.SELECTOR/R/run_REFERENCE.SAMPLE.SET.SELECTOR.R
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| run_REFERENCE.SAMPLE.SET.SELECTOR <- function(investigated_sample, | ||
| Y, | ||
| select_method, | ||
| num_refs, | ||
| target_length){ | ||
| if(select_method == "canoes") { | ||
| reference_samples <- canoes_method(investigated_sample, Y, num_refs)$reference_samples | ||
| } else if(select_method == "codex") { | ||
| #reference_samples <- codex_method(investigated_sample, Y, num_refs)$reference_samples | ||
| } else if(select_method == "exomedepth") { | ||
| reference_samples <- exomedepth_method(investigated_sample, Y, num_refs, target_length)$reference_samples | ||
| } else if(select_method == "clamms") { | ||
| #reference_samples <- clamms_method(investigated_sample, Y, num_refs)$reference_samples | ||
| } | ||
| reference_samples | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,111 @@ | ||
| library(testthat) | ||
| library(REFERENCE.SAMPLE.SET.SELECTOR) | ||
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| context("Testing canoes_method function") | ||
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| test_that("basic test for canoes_method function with num_refs equal to 5",{ | ||
| investigated_sample <- "sample_1" | ||
| num_refs <- 5 | ||
| Y = matrix(as.integer(c(52, 53, 54, 56, 70, 147, 58, 51, | ||
| 25, 22, 39, 31, 27, 217, 17, 27, | ||
| 57, 61, 66, 65, 64, 177, 67, 59, | ||
| 101, 100, 90, 85, 98, 182, 92, 103, | ||
| 149, 154, 140, 160, 165, 213, 149, 162, | ||
| 95, 90, 90, 98, 88, 262, 93, 103, | ||
| 50, 55, 45, 52, 59, 135, 65, 55, | ||
| 79, 57, 63, 90, 71, 216, 69, 66)), nrow=8, ncol=8, byrow = TRUE) | ||
| colnames(Y) <- c("sample_1", "sample_2", "sample_3", "sample_4", "sample_5", "sample_6", "sample_7", "sample_8") | ||
| reference_samples <- canoes_method(investigated_sample, | ||
| Y, | ||
| num_refs) | ||
| expect_equal(length(reference_samples), 1) | ||
| expect_equal(length(reference_samples$reference_samples), num_refs) | ||
| expect_equal(reference_samples$reference_samples[1], 'sample_8') | ||
| expect_equal(reference_samples$reference_samples[2], 'sample_4') | ||
| expect_equal(reference_samples$reference_samples[3], 'sample_2') | ||
| expect_equal(reference_samples$reference_samples[4], 'sample_3') | ||
| expect_equal(reference_samples$reference_samples[5], 'sample_7') | ||
| }) | ||
|
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| test_that("basic test for canoes_method function with num_refs equal to 0",{ | ||
| investigated_sample <- "sample_1" | ||
| num_refs <- 0 | ||
| Y = matrix(as.integer(c(52, 53, 54, 56, 70, 147, 58, 51, | ||
| 25, 22, 39, 31, 27, 217, 17, 27, | ||
| 57, 61, 66, 65, 64, 177, 67, 59, | ||
| 101, 100, 90, 85, 98, 182, 92, 103, | ||
| 149, 154, 140, 160, 165, 213, 149, 162, | ||
| 95, 90, 90, 98, 88, 262, 93, 103, | ||
| 50, 55, 45, 52, 59, 135, 65, 55, | ||
| 79, 57, 63, 90, 71, 216, 69, 66)), nrow=8, ncol=8, byrow = TRUE) | ||
| colnames(Y) <- c("sample_1", "sample_2", "sample_3", "sample_4", "sample_5", "sample_6", "sample_7", "sample_8") | ||
| reference_samples <- canoes_method(investigated_sample, | ||
| Y, | ||
| num_refs) | ||
| expect_equal(length(reference_samples), 1) | ||
| expect_equal(length(reference_samples$reference_samples), 7) | ||
| expect_equal(reference_samples$reference_samples[1], 'sample_8') | ||
| expect_equal(reference_samples$reference_samples[2], 'sample_4') | ||
| expect_equal(reference_samples$reference_samples[3], 'sample_2') | ||
| expect_equal(reference_samples$reference_samples[4], 'sample_3') | ||
| expect_equal(reference_samples$reference_samples[5], 'sample_7') | ||
| expect_equal(reference_samples$reference_samples[6], 'sample_5') | ||
| expect_equal(reference_samples$reference_samples[7], 'sample_6') | ||
| }) | ||
|
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| context("Testing exomedepth_method function") | ||
|
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| test_that("basic test for exomedepth_method function with num_refs equal to 5",{ | ||
| investigated_sample <- "sample_1" | ||
| num_refs <- 5 | ||
| target_length <- c(1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000) | ||
| Y = matrix(as.integer(c(52, 53, 54, 56, 70, 147, 58, 51, | ||
| 25, 22, 39, 31, 27, 217, 17, 27, | ||
| 57, 61, 66, 65, 64, 177, 67, 59, | ||
| 101, 100, 90, 85, 98, 182, 92, 103, | ||
| 149, 154, 140, 160, 165, 213, 149, 162, | ||
| 95, 90, 90, 98, 88, 262, 93, 103, | ||
| 50, 55, 45, 52, 59, 135, 65, 55, | ||
| 79, 57, 63, 90, 71, 216, 69, 66)), nrow=8, ncol=8, byrow = TRUE) | ||
| colnames(Y) <- c("sample_1", "sample_2", "sample_3", "sample_4", "sample_5", "sample_6", "sample_7", "sample_8") | ||
| reference_samples <- exomedepth_method(investigated_sample, | ||
| Y, | ||
| num_refs, | ||
| target_length) | ||
| expect_equal(length(reference_samples), 1) | ||
| expect_equal(length(reference_samples$reference_samples), num_refs) | ||
| expect_equal(reference_samples$reference_samples[1], 'sample_8') | ||
| expect_equal(reference_samples$reference_samples[2], 'sample_4') | ||
| expect_equal(reference_samples$reference_samples[3], 'sample_5') | ||
| expect_equal(reference_samples$reference_samples[4], 'sample_2') | ||
| expect_equal(reference_samples$reference_samples[5], 'sample_3') | ||
| }) | ||
|
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| test_that("basic test for exomedepth_method function with num_refs equal to 0 (auto)",{ | ||
| investigated_sample <- "sample_1" | ||
| num_refs <- 0 | ||
| target_length <- c(1000, 1000, 1000, 1000, 1000, 1000, 1000, 1000) | ||
| Y = matrix(as.integer(c(52, 53, 54, 56, 70, 147, 58, 51, | ||
| 25, 22, 39, 31, 27, 217, 17, 27, | ||
| 57, 61, 66, 65, 64, 177, 67, 59, | ||
| 101, 100, 90, 85, 98, 182, 92, 103, | ||
| 149, 154, 140, 160, 165, 213, 149, 162, | ||
| 95, 90, 90, 98, 88, 262, 93, 103, | ||
| 50, 55, 45, 52, 59, 135, 65, 55, | ||
| 79, 57, 63, 90, 71, 216, 69, 66)), nrow=8, ncol=8, byrow = TRUE) | ||
| colnames(Y) <- c("sample_1", "sample_2", "sample_3", "sample_4", "sample_5", "sample_6", "sample_7", "sample_8") | ||
| reference_samples <- exomedepth_method(investigated_sample, | ||
| Y, | ||
| num_refs, | ||
| target_length) | ||
| expect_equal(length(reference_samples), 1) | ||
| expect_equal(length(reference_samples$reference_samples), 6) | ||
| expect_equal(reference_samples$reference_samples[1], 'sample_8') | ||
| expect_equal(reference_samples$reference_samples[2], 'sample_4') | ||
| expect_equal(reference_samples$reference_samples[3], 'sample_5') | ||
| expect_equal(reference_samples$reference_samples[4], 'sample_2') | ||
| expect_equal(reference_samples$reference_samples[5], 'sample_3') | ||
| expect_equal(reference_samples$reference_samples[6], 'sample_7') | ||
| }) | ||
|
|
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