spline_coefs: calculates the median-centered x's positions by spline points

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

calculates the median-centered x's positions by spline points

Description

Only used with method_align = MC. The values of x's for sample IDs indicated in label_scheme_fit will be updated for subsequent adjustment in median centering. The rest of x's stays the same, corresponding to no further changes in center positions.

Usage

spline_coefs(
  df,
  label_scheme,
  label_scheme_fit,
  is_prot_lfq = FALSE,
  method_align = "MC",
  ...
)

Arguments

df	A data frame.
label_scheme	The metadata of label scheme.
label_scheme_fit	the subset of label_scheme used in fitting.
is_prot_lfq	Logical; is protein LFQ data or not. About half of the protein intensity values can be missing with LFQ and imputed with small values. The typically causes a bimodality in protein log2FC distributions and need to be handled especially at method_align = "MC".
method_align	Character string indicating the method in aligning log2FC across samples. MC: median-centering; MGKernel: the kernel density defined by multiple Gaussian functions (normalmixEM). At the MC default, the ratio profiles of each sample will be aligned in that the medians of the log2FC are zero. At MGKernel, the ratio profiles of each sample will be aligned in that the log2FC at the maximums of kernel density are zero.
...	Additional parameters, including slice_dots.

qzhang503/proteoQ documentation built on April 13, 2025, 8:31 a.m.