Merge branch 'master' of github.com:jromanowska/HaplinMethyl

R/findCpGsnearSNP.R

@@ -1,18 +1,28 @@
 #' Finding CpGs near a SNP
 #'
-#' This is a basic function for searching for CpGs in the vicinity of a given SNP
+#' @description 
+#' This is a basic function for searching for CpGs in the vicinity of a given
+#' SNP.
 #'
-#' Given a position and chromosome number of a SNP, along with a table of
-#'   positions of CpGs in this chromosome, the function will return a data.frame
-#'   with nearby CpGs (within a given limit).
+#' @details 
+#' Given the position and chromosome number of a SNP, along with the positions
+#' of CpGs on the same chromosome, the function will return a data.frame with
+#' nearby CpGs (within a given number of base pairs).
+#'  
+#' **Please note** that you should ensure that every CpG in `cpgs` and the SNP
+#'  in `snp` are located on the same chromosome.
 #'
-#' @param snp A named list with SNP name ("marker"), chromosome no. ("chr")
+#' @param snp A named list with the SNP's name ("marker"), chromosome no. ("chr")
 #'     and coordinate ("coord").
-#' @param cpgs A table with all CpGs in a given chromosome, with the columns
-#'     named: "id", "coord".
-#' @param range Number giving the maximum distance from the SNP where the
-#'    function will look for CpGs; default: 5000 (base pairs).
-#' @param verbose Whether to display extra info about each SNP (default: FALSE).
+#' @param cpgs A list or data.frame containing all CpGs on the chromosome where
+#'   the SNP is located. Must contain only two elements/columns: one named "id" 
+#'   (unique CpG locus cluster ID, cg#) and one named "coord" (coordinate of CpG
+#'    locus).
+#' @param range An integer specifying the desired maximum number of base pairs
+#'   between the given SNP and CpGs. The default is 5000. The search for CpGs is
+#'   restricted to the interval (snp$coord - range, snp$coord + range).
+#' @param verbose Whether to print information about the result when available
+#'   (default: FALSE).
 #'
 #' @return A data.frame with CpGs with columns named: "id", "coord".
 #'
@@ -28,8 +38,20 @@ findCpGsnearSNP <- function( snp = stop( "'snp' is required!", call. = FALSE ),
 			  including the marker name ('marker'), chromosome number ('chr'),
 			  and the coordinate ('coord').", call. = FALSE )
 	}
+  if( is.recursive( cpgs ) == FALSE ){
+    stop( "The given argument 'cpgs' is not compatible with the $ operator. 
+          'cpgs' must be a recursive (list-like) object such as a data frame, 
+          list or tibble."
+          , call. = FALSE )
+  }
+	if( !( length(names( cpgs )) == 2)  ){
+		stop( paste( "The given 'cpgs' must be a list or data.frame with exactly 2",
+		             "elements or columns!"),
+			  call. = FALSE )
+	}
 	if( !all(names( cpgs ) %in% c( "id", "coord" )) ){
-		stop( "The given 'cpg' must be a data.frame with the columns named 'id' and 'coord'!",
+	  stop( paste( "The given 'cpgs' must be a list or data.frame with exactly 2",
+	               "elements or columns named 'id' and 'coord'!"),
 			  call. = FALSE )
 	}