Rebuild vignettes in inst/doc

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2024-03-03
+Date: 2024-03-04
 Package: canprot
-Version: 1.1.2-30
+Version: 1.1.2-31
 Title: Chemical Analysis of Proteins
 Authors@R: c(
     person("Jeffrey", "Dick", email = "[email protected]", role = c("aut", "cre"),

R/read.fasta.R

@@ -147,13 +147,23 @@ count.aa <- function(sequence, start = NULL, stop = NULL, type = "protein") {
 aasum <- function(AAcomp, abundance = 1, average = FALSE) {
   # Recycle abundance values into same length as number of proteins
   abundance <- rep(abundance, length.out = nrow(AAcomp))
-  # Find columns with names for the amino acids and "chains"
+  # Find columns with names for the amino acids and 'chains'
+  # (number of polypeptide chains)
   AA_names <- c(
     "Ala", "Cys", "Asp", "Glu", "Phe", "Gly", "His", "Ile", "Lys", "Leu",
     "Met", "Asn", "Pro", "Gln", "Arg", "Ser", "Thr", "Val", "Trp", "Tyr",
     "chains"
   )
   isAA <- tolower(colnames(AAcomp)) %in% tolower(AA_names)
+  # Remove proteins with NA amino acid composition or abundance
+  ina.aa <- is.na(rowSums(AAcomp[, isAA]))
+  ina.ab <- is.na(abundance)
+  ina <- ina.aa | ina.ab
+  if (any(ina)) {
+      AAcomp <- AAcomp[!ina, ]
+      abundance <- abundance[!ina]
+      message("aasum: dropped ", sum(ina), " proteins with NA amino acid composition and/or abundance")
+  }
   # Multiply amino acid counts by protein abundance
   AAcomp[, isAA] <- AAcomp[, isAA] * abundance
   # Sum amino acid counts

README.md

@@ -46,4 +46,4 @@ demo("canprot")
 <img src="inst/images/canprot.png" alt="Zc and pI for human proteins in subcellular locations" title="canprot demo" width="600px" />
 
 These plots show carbon oxidation state (*Z*<sub>C</sub>) and isoelectric point (pI) for human proteins in different subcellular locations.
-The localization data is from Table S6 of [Thul et al. (2017)](10.1126/science.aal3321) (*A subcellular map of the human proteome*), filtered to include proteins that have both a validated location and only one predicted location.
+The localization data is from Table S6 of [Thul et al. (2017)](https://doi.org/10.1126/science.aal3321) (*A subcellular map of the human proteome*), filtered to include proteins that have both a validated location and only one annotated location.

inst/NEWS

@@ -1,4 +1,4 @@
-CHANGES IN canprot 1.1.2-29 (2024-03-03)
+CHANGES IN canprot 1.1.2-30 (2024-03-03)
 ----------------------------------------
 
 - Objects in cplab are now `quote()`-ed instead of `expression()`s for easier