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# rBiasCorrection: Correct Bias in Quantitative DNA Methylation Analyses.
# Copyright (C) 2019-2022 Lorenz Kapsner
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# create aggregated datatable for calibration data
create_agg_df <- function(datatable,
index) {
df <- datatable[, c("true_methylation", index), with = FALSE]
colnames(df)[2] <- "CpG"
df_out <- df[, ("true_methylation") := as.numeric(
as.character(
get("true_methylation")
)
)]
df_out <- df[
,
list(
"CpG" = mean(get("CpG"), na.rm = TRUE),
"sd" = stats::sd(get("CpG"), na.rm = TRUE)
),
by = "true_methylation"
]
if (df_out[is.na(get("sd")), .N] == nrow(df_out)) {
df_out[, ("sd") := NULL]
}
return(df_out[!is.na(get("CpG")), ])
}
# create aggregated datatable for experimental data
create_agg_df_exp <- function(datatable,
index,
type) {
if (type == 1) {
df <- datatable[, c("sample_id", index), with = FALSE]
colnames(df)[2] <- "CpG"
df_out <- df[
,
list(
"CpG" = mean(get("CpG"), na.rm = TRUE),
"sd" = stats::sd(get("CpG"), na.rm = TRUE)
),
by = "sample_id"
]
} else if (type == 2) {
df <- datatable[, c("locus_id", index), with = FALSE]
colnames(df)[2] <- "CpG"
df_out <- df[
,
list(
"CpG" = mean(get("CpG"), na.rm = TRUE),
"sd" = stats::sd(get("CpG"), na.rm = TRUE)
),
by = "locus_id"
]
}
if (df_out[is.na(get("sd")), .N] == nrow(df_out)) {
df_out[, ("sd") := NULL]
}
return(df_out[!is.na(get("CpG")), ])
}
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