analNMF: NMF analysis

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

NMF analysis

Description

NMF analysis

Usage

analNMF(
  df,
  id,
  rank,
  nrun,
  seed,
  col_group,
  label_scheme_sub,
  scale_log2r,
  complete_cases,
  impute_na,
  filepath,
  filename,
  anal_type,
  ...
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
rank	Numeric vector; the factorization rank(s) in nmf. The default is c(4:8)
nrun	Numeric; the number of runs in nmf. The default is 50.
seed	Integer; a seed for reproducible analysis.
col_group	Character string to a column key in expt_smry.xlsx. Samples corresponding to non-empty entries under col_group will be used for sample grouping in the indicated analysis. At the NULL default, the column key Group will be used. No data annotation by groups will be performed if the fields under the indicated group column is empty.
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.
scale_log2r	Logical; if TRUE, adjusts log2FC to the same scale of standard deviation across all samples. The default is TRUE. At scale_log2r = NA, the raw log2FC without normalization will be used.
complete_cases	Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE.
impute_na	Logical; if TRUE, data with the imputation of missing values will be used. The default is TRUE.
filepath	Use system default.
filename	A representative file name to outputs. By default, it will be determined automatically by the name of the current call.
anal_type	Character string; the type of analysis that are preset for method dispatch in function factories. The value will be determined automatically. Exemplary values include anal_type = c("PCA", "Corrplot", "EucDist", "GSPA", "Heatmap", "Histogram", "MDS", "Model", "NMF", "Purge", "Trend", "LDA", ...).
...	filter_: Logical expression(s) for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements. arrange_: Variable argument statements for the row ordering against data in a primary file linked to df. See also prnHM for the format of arrange_ statements. Additional arguments for nmf.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.