use R.utils to count number of SNPs from *.bim file.

umr1283 · May 4, 2020 · da3b572 · da3b572
1 parent 6ab0cf7
commit da3b572
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rain
 Title: Reference-based Ancestry INference
-Version: 0.3.4
+Version: 0.3.5
 Authors@R: 
     c(person(given = "Mickaël",
              family = "Canouil",
@@ -34,6 +34,7 @@ Imports:
     purrr (>= 0.3.3),
     readr (>= 1.3.1),
     rlang (>= 0.4.2),
+    R.utils (>= 2.9.2),
     scales (>= 1.1.0),
     tibble (>= 2.1.3),
     tidyr (>= 1.0.0),

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,12 @@
 
 ## Minor improvements and fixes
 
+* In `R/compute_pca.R`, use `R.utils` to count number of SNPs from `*.bim` file.
+
+# rain 0.3.4
+
+## Minor improvements and fixes
+
 * In `R/compute_pca.R`, fix number of SNPs in ggplot legend.
 
 # rain 0.3.3

diff --git a/R/compute_pca.R b/R/compute_pca.R
@@ -140,7 +140,7 @@ compute_pca <- function(cohort_name, input_plink, output_directory, ref1kg_popul
       title = "Estimated Ethnicity",
       subtitle = paste(
         "Based on Principal Component Analysis using",
-        scales::comma(ncol(res_pca[["projection"]])),
+        scales::comma(R.utils::countLines(paste0(input_plink, ".bim"))),
         "SNPs."
       )
     )