collapseIntesity: Collapse rows of an intensity matrix according to a...

In mengchen18/proturn: System-wise protein turnover curve fitting

Description

Collapse rows of an intensity matrix according to a vector/factor.

Usage

collapseIntesity(x, intensity.col, collapse.col = "Sequence", annot.col,
  n.cores = 1, collapse.method = c("sum", "mean", "median", "max.range",
  "max.range01")[1])

Arguments

x	a data.frame containing at least the intensity columns and a column according to which intensities are collapsed.
intensity.col	the columns of intensities, could be either column names or column indices
collapse.col	the column accroding to which intensity are collapsed. Most of the cases, this column should be peptide sequences or protein IDs, see details.
annot.col	the annotation columns, which will be retained in the output.
n.cores	the number of cores to be used, it is passed to mclapply
collapse.method	the collapse method, see details section.

Details

This function prepares input for fitDegNLS. Two typical usages are: 1) collapse intensitys on peptide level, i.e. if multiple rows corresponds to identical peptide, combine them into one rows in some way (see below). In this case, the peptide sequence should be used as collapse.col. 2) collapse from peptide level to protein levels, so the protein name or ID could be used as collapse.col.

The following collapse methods are avaliable:

• sum sum the intensities;

• mean mean of intensities;

• median median of intensities;

• max.range retain the one with max range;

• max.range01 retain the one with max difference between first and last intensity columns.

Value

a data.frame of collapsed intensities, containing the collapsed.col, intensity.col and annot.cols.

Author(s)

Chen Meng

Examples

  df <- data.frame(
    sequence = c("CCAD", "CSDS", "IIURE", "IIURE", "XMNT"),
    t0 = rnorm(5),
    t1 = rnorm(5),
    t2 = rnorm(5),
    name = LETTERS[1:5]
  )
  collapseIntesity(x = df, collapse.col = "sequence", intensity.col = c("t0", "t1", "t2"), annot.col = "name")
  collapseIntesity(x = df, collapse.col = 1, intensity.col = 2:4, annot.col = 5, collapse.method = "max.range01")

mengchen18/proturn documentation built on May 30, 2019, 4:37 p.m.