date_to_sample_order: Convert date/time to POSIXct and rank samples by it

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Convert date/time to POSIXct and rank samples by it

Description

Converts date/time columns fo sample_annotation to POSIXct format and calculates sample run rank in order column

Usage

date_to_sample_order(sample_annotation, time_column = c("RunDate",
  "RunTime"), new_time_column = "DateTime",
  dateTimeFormat = c("%b_%d", "%H:%M:%S"),
  new_order_col = "order", instrument_col = "instrument")

Arguments

sample_annotation	data frame with: sample_id_col (this can be repeated as row names) biological covariates technical covariates (batches etc) . See help("example_sample_annotation")
time_column	name of the column(s) where run date & time are specified. These will be used to determine the run order
new_time_column	name of the new column to which date&time will be converted to
dateTimeFormat	POSIX format of the date and time. See as.POSIXct from base R for details
new_order_col	name of column with generated the order of sample run based on time columns
instrument_col	column, denoting different instrument used for measurements

Value

sample annotation file with a new column new_time_column with POSIX-formatted date & new_order_col used in some diagnostic plots (e.g. plot_iRT, plot_sample_mean)

Examples

sample_annotation_wOrder <- date_to_sample_order(
example_sample_annotation,
time_column = c('RunDate','RunTime'),
new_time_column = 'new_DateTime',
dateTimeFormat = c("%b_%d", "%H:%M:%S"),
new_order_col = 'new_order',
instrument_col = NULL)

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.