In mooredf22/protlocassign0p1p1: Compute constrained proportional assignments for fractionated protein abundance

knitr::opts_chunk$set(
  #collapse = TRUE,
  comment = "#>",
  fig.width = 4,
  fig.height = 4,
  message = FALSE,
  warning = FALSE,
  tidy.opts = list(
    keep.blank.line = TRUE,
    width.cutoff = 150
  ),
  options(width = 150),
  eval = TRUE
)

Finding proteins with similar profiles

We may find the proteins with profiles nearest to a given protein using the function "nearestProts". Distance is computed as the Euclidean distance between profiles. To use the function, we first use the R function dist to create a distance matrix for the proteins in a list of mean profiles, such as protProfileNSA_AT5tmtMS2. For clarity of presentation, we rename the embedded data sets to remove experiment-specific labels.

library(protlocassign)
data(protNSA_AT5tmtMS2)
data(totProtAT5)
protNSA <- protNSA_AT5tmtMS2
totProt <- totProtAT5
distUseNSA <- dist(protNSA[,1:9], method="euclidean")

Then select the protein names:

protsUse <- rownames(protNSA)

Finally, provide a protein name. Here, for the protein "CTSD", we find the 10 nearest proteins.

nearestProts(protName="CTSD", n.nearest=10,  distProts=distUseNSA, protNames=protsUse,
             profile=protNSA)

Instead of using normalized specific amounts, we may transform them to relative specific amounts:

protProfileLevelsRSA <- RSAfromNSA(NSA=protNSA[,1:9],
                                 NstartMaterialFractions=6, totProt=totProt)
distUseRSA <- dist(protProfileLevelsRSA, method="euclidean")
nearestProts(protName="CTSD", n.nearest=10,  distProts=distUseRSA, protNames=protsUse,
             profile=protProfileLevelsRSA)

Note that if one wants to generate a table listing the distances between all protein pairs, one needs to convert the distUse or distUseRSA to a matrix. We show the first five rows and columns here:

distUseNSAmatrix <- as.matrix(distUseNSA)
distUseNSAmatrix[1:5,1:5]

This matrix can be written to a local directory using standard procedures.

mooredf22/protlocassign0p1p1 documentation built on Feb. 7, 2022, 1:55 a.m.