dea: Differential expression analysis

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Differential expression analysis

Description

Differential expression analysis

Usage

dea(
  dataset,
  qval_signif = 0.01,
  fc_signif = 0,
  dea_algorithm = "deqms",
  rollup_algorithm = "maxlfq",
  output_dir_for_eset = ""
)

Arguments

dataset	your dataset
qval_signif	threshold for significance of q-values
fc_signif	threshold for significance of log2 foldchanges. Set to zero or NA to disregard, or a positive value to apply a cutoff to absolute log2 foldchanges. MS-DAP can also perform a bootstrap analyses to infer a reasonable threshold by setting this parameter to NA
dea_algorithm	algorithm for differential expression analysis (provide an array of strings to run multiple, in parallel). Refer to dea_algorithms function documentation for available options and a brief description of each. To use a custom DEA function, provide the respective R function name as a string (see GitHub documentation on custom DEA functions for more details)
rollup_algorithm	algorithm for combining peptides to proteins as used in DEA algorithms that require a priori rollup from peptides to a protein-level abundance matrix before applying statistics (e.g. ebayes, deqms). Refer to rollup_pep2prot function documentation for available options and a brief description of each
output_dir_for_eset	optionally, provide an output directory where the expressionset objects should be stored. Only useful if you're doing downstream data analysis that requires this data

Value

long-format tibble with results for each DEA algorithm requested via dea_algorithm parameter. Note that a MS-DAP contrast for "A vs B" returns foldchanges for B/A. For example, for the contrast "control vs disease" a positive log2 foldchange implies protein abundances are higher in the "disease" sample group. The column signif contains a boolean flag indicating significant hits according to both the user defined q-value threshold (parameter qval_signif, also in result table column signif_threshold_qvalue) and optional foldchange threshold (parameter fc_signif, also in result table column signif_threshold_log2fc)

See Also

dea_algorithms() for available DEA algorithms and documentation.

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.