getFragmentsDistribution {VplotR} | R Documentation |
This function takes fragments and compute the distribution of their sizes over a set or multiple sets of GRanges.
getFragmentsDistribution( fragments, granges_list = NULL, extend_granges = c(-500, 500), limits = c(0, 600), roll = 3, cores = 1 )
fragments |
GRanges object containing paired-end fragments. See importPEBamFiles for more details on how to create such object. |
granges_list |
GRanges, can be a list of different sets of GRanges. |
extend_granges |
numeric vector of length 2, how the GRanges should be extended. |
limits |
numeric vector of length 2, only consider fragments within this window of sizes. |
roll |
Integer, apply a moving average of this size |
cores |
Integer, number of threads used to compute fragment size distribution |
A list of tbl, one for each .bam file.
data(bam_test) data(ce11_proms) df <- getFragmentsDistribution( bam_test, ce11_proms, extend_granges = c(-500, 500) ) head(df) which.max(df$y)