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#' Calculate the metrics of insert size
#'
#' @importFrom magrittr %>%
#' @import dplyr
#' @param path The root folder containing all groups folders,
#' default is the present working folder.
#' @param groups The name of the groups, the input value should be vector,
#' e.g. groups=c('group1','group2'),
#' default is all sub-folders in the 'path'.
#' @param fun String value, the types of metrics to be calculated.
#' Default is 'all', which means both median and mean values
#' will be returned.
#' @param outfmt The output format, a 'list' or 'dataframe' or 'df',
#' default is dataframe.
#' @param input_type Character. The input file format,
#' should be one of these: 'picard', 'bam'. The bam files has to be
#' marked duplicates.
#' @param ... Further arguments passed to or from other methods.
#' @return The inter valley distance in list or dataframe format.
#' @examples
#' # Get the path to example data.
#' path <- examplePath("groups_picard")
#' # Calculate the metrics.
#' df <- callMetrics(path = path)
#' @author Haichao Wang
#' @export
callMetrics <-
function(path = getwd(),
groups,
fun = "all",
outfmt = "df",
input_type,
...) {
if (missing(groups)) {
groups <- list.dirs(
path = path,
recursive = FALSE,
full.names = FALSE
)
}
if (missing(input_type)) {
input_type <- "picard"
cat("setting default input_type to picard.\n")
}
if (fun == "all" & outfmt == "df") {
result <-
AllGroupPropCdfMeanMedian_Dataframe(
path = path,
groups = groups,
input_type = input_type,
...
)
} else if (fun == "all" & outfmt == "list") {
result <-
AllGroupPropCdfMeanMedian_List(
path = path,
groups = groups,
input_type = input_type,
...
)
} else if (fun == "median" & outfmt == "df") {
result <-
AllGroupPropCdfMeanMedian_Dataframe(
path = path,
groups = groups,
input_type = input_type,
...
) %>% select(-ends_with("mean"))
} else if (fun == "median" & outfmt == "list") {
result <-
AllGroupPropCdfMeanMedian_List(
path = path,
groups = groups,
input_type = input_type,
...
) %>%
lapply(select, -ends_with("mean"))
} else if (fun == "mean" & outfmt == "df") {
result <-
AllGroupPropCdfMeanMedian_Dataframe(
path = path,
groups = groups,
input_type = input_type,
...
) %>%
select(-ends_with("median"))
} else if (fun == "mean" & outfmt == "list") {
result <-
AllGroupPropCdfMeanMedian_List(
path = path,
groups = groups,
input_type = input_type,
...
) %>%
lapply(select, -ends_with("median"))
}
return(result)
}
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