SpectroPipeR: loading Spectronaut data module — read_spectronaut

Function for loading Spectronaut data and performing identification (ID) analysis, which is an essential first step in the SpectroPipeR workflow.

Usage

read_spectronaut_module(
  file = "",
  ID_condition_filtering = FALSE,
  ID_condition_filtering_percent = 0.5,
  parameter = list(),
  max_chars_file_name_capping = 35,
  print.plot = FALSE,
  report_copy = F
)

Arguments

file

location (path) of Spectronaut output report; you should use the Spectronaut_export_scheme() function for getting a SpectroPipeR report scheme encompassing all mandatory columns

ID_condition_filtering

TRUE or FALSE if a condition-wise filtering should be performed

ID_condition_filtering_percent

(numerical value ranging from 0 - 1, default = 0.5) define the proportion for the condition-wise ID filtering

parameter

mandatory parameter list element

table of list elements:

parameter	description
output_folder	mandatory !!! - character - output folder path (abs.)
ion_q_value_cutoff	default = 0.01 - numeric - Q-value used in Spectronaut analysis: Biognosys
	default is 0.01 = 1% error rate
id_drop_cutoff	default = 0.3 - numeric - value between 0-1 (1 = 100%); xx percent lower
	than median of ion ID rate => outlier
normalization_method	default = "median" - character - "median" or Spectronaut - auto-detection
	is per default ON, meaning if normalization was performed in Spectronaut
	this will be detected and preferred over parameter setting here;
	median normalization is the fallback option
normalization_factor_cutoff_outlier	default = 4 - numeric - median off from global median
	(4 means abs. 4fold off)
filter_oxidized_peptides	default = TRUE logical - if oxidized peptides should be removed before
	peptide quantification
protein_intensity_estimation	default = "MaxLFQ" - character - Hi3 = Hi3 protein intensity estimation,
	MaxLFQ = MaxLFQ protein intensity estimation
stat_test	default = "rots" - character - choose statistical test: "rots" = reproducibility
	optimized test statistics, "modt" = moderate t-test (lmfit, eBayes),
	"t" = t-test
type_slr	default = "median" - character - choose ratio aggregation method:
	"median" or "tukey" is used when calculating protein values
fold_change	default = 1.5 - numeric - fold-change used as cutoff e.g. 1.5
p_value_cutoff	default = 0.05 - numeric - p-value used as cutoff e.g. 0.05
paired	default = FALSE - logical - Should paired statistics be applied?

example parameters list (default):

params <- list(output_folder = "../Spectronaut_example",

ion_q_value_cutoff = 0.01,

id_drop_cutoff = 0.3,

normalization_method = "median",

normalization_factor_cutoff_outlier = 4,

filter_oxidized_peptides = T,

protein_intensity_estimation = "MaxLFQ",

stat_test = "rots",

type_slr = "median",

fold_change = 1.5,

p_value_cutoff = 0.05,

paired = FALSE

)

max_chars_file_name_capping

integer, (default = 35) number of max characters used for raw file name presentation; must be adjusted if function

print.plot

if TRUE –> printing ID plot on ion level coloring corresponds ID outlier estimate by "id_drop_cutoff" variable

report_copy

if TRUE –> copy Spectronaut input report to SpectroPipeR project folder 01_input_data

Value

SpectroPipeR_data list object with the loaded raw data and processed data tables, in addition to the automatically saved tables and plots. For the description of the generated figures and tables please read the manual & vignettes

list element	description
spectronaut_output	tibble: Spectronaut report tibble provided for the analysis
SDRF_file	tibble: intermediate SDRF table of the analysis
summary_distinct	tibble: distinct ion, modified peptide, stripped peptides and
	protein group count per file filtered by provided Q-value
raw_file_names	tibble: R.FileNames capped and uncapped version together with
	R.Condition and R.Replicate
ion_id_median	numerical value: median of ion intensity
ion_id_cutoff	numerical value: ion ID count threshold to classify sample as outlier
PG_2_peptides_ID_raw	tibble: with protein groups with at least 2 peptides with peptide
	and replicate count
summary_distinct_outlier	tibble: if outlier are detected they are listed in this tibble
ID_rate_plot	ggplot2 plot: ID rate plot
ID_rate_plot_filter	ggplot2 plot: ion ID rate plot with ion ID cutoff line
sample_length	numberical value: number of samples in the provided Spectronaut report
parameter	list: parameters provided by the user
time_stamp_log_file	string: time stamp of the log file (format: %Y_%m_%d__%H_%M)
log_file_name	string: analysis log file name

Examples

# \donttest{
#load library
library(SpectroPipeR)

# use default parameters list
params <- list(output_folder = "../SpectroPipeR_test_folder")

# example input file
example_file_path <- system.file("extdata",
                                "SN_test_HYE_mix_file.tsv",
                                package="SpectroPipeR")

# step 1: load Spectronaut data module
SpectroPipeR_data <- read_spectronaut_module(file = example_file_path,
                                            parameter = params,
                                            print.plot = FALSE)
# }