diff --git a/DESCRIPTION b/DESCRIPTION index fde5c6b..d624b9d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Ibex Title: Methods for BCR single-cell embedding -Version: 1.1.1 +Version: 1.3.2 Authors@R: c( person(given = "Nick", family = "Borcherding", role = c("aut", "cre", "cph"), email = "ncborch@gmail.com"), person(given = "Qile", family = "Yang", role = "ctb", email = "qile.yang@berkeley.edu", comment = c(ORCID = "0009-0005-0148-2499"))) diff --git a/NEWS.md b/NEWS.md index 3885d4e..9887db1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,25 +1,19 @@ # Ibex - Change Log +## v1.3.2 + +* Fixed inverted boolean condition check for `.EXP` models in `Ibex_matrix` + +## v1.3.1 + +* Realign versioning again with Bioconductor release + ## v1.1.1 * Aligned version with Bioconductor release * Switched default branch to `devel` for Bioconductor compatibility * Updated CI workflows to target `devel` branch * Converted NEWS to NEWS.md format * Added automated GitHub Release workflow via tags - -## v1.0.0 -* Integration of Ibex with immApex -* Updated Seurat object to v5 -* Updated support for SCE format for `runIbex()` -* Update `CoNGAfy()` to function with all versions of Seurat -* Updated `quietBCRgenes()` to use VariableFeatures() call for SeuratV5 and backward compatibility -* Added `getHumanIgPseudoGenes()` to return a list of human Immunoglobulin Pseudo genes -* Added new light and heavy chain models with encoding methods: OHE, atchleyFactors, crucianiProperties, kideraFactors, MSWHIM, tScales, zScales -* Trained convolutional and variational autoencoders (architecture: 512-256-128-256-512) -* Implementing GitHub action workflows -* Adding testthat framework -* Deprecated clonalCommunity -* Added geometric encoding using the BLOSUM62 matrix * `Ibex_matrix()` now accepts character vectors of amino acid sequences directly * Removed rlang from Imports, added lifecycle * As per `basilisk` documentation: diff --git a/R/Ibex_matrix.R b/R/Ibex_matrix.R index 3b23b7d..3e4922e 100644 --- a/R/Ibex_matrix.R +++ b/R/Ibex_matrix.R @@ -102,9 +102,9 @@ Ibex_matrix <- function(input.data, # Determine dictionary for sequence encoding if (expanded.sequences) { #Quick Check to see if there are - corresponding to CDR1-CDR2-CDR3 - if (all(grepl("-", BCR[,"cdr3_aa"]))) { + if (!all(grepl("-", BCR[,"cdr3_aa"]))) { stop("Expanded sequences are not properly formated, please use - combineExpandedBCR().") + combineExpandedBCR() or ensure each element is CDRs 1, 2, and 3 joined by `-`") } BCR[,"cdr3_aa"] <- gsub("-", "_", BCR[,"cdr3_aa"]) dictionary <- c(amino.acids, "_")