| shiftFootprintsByExperiment {ORFik} | R Documentation |
Saves files to a specified location as .bed, it will include a score column containing read width.
shiftFootprintsByExperiment( df, out.dir = pasteDir(dirname(df$filepath[1]), "/pshifted/"), start = TRUE, stop = FALSE, top_tx = 10L, minFiveUTR = 30L, minCDS = 150L, minThreeUTR = 30L, firstN = 150L, min_reads = 1000, accepted.lengths = 1:1000, output_format = "bed" )
df |
an ORFik |
out.dir |
output directory for files, default: dirname(df$filepath[1]), making a /pshifted folder at that location |
start |
(logical) Whether to include predictions based on the start codons. Default TRUE. |
stop |
(logical) Whether to include predictions based on the stop codons. Default FASLE. Only use if there exists 3' UTRs for the annotation. If peridicity around stop codon is stronger than at the start codon, use stop instead of start region for p-shifting. |
top_tx |
(integer) Specify which transcripts to use for estimation of the shifts. By default we take top 10 top covered transcripts as they represent less noisy dataset. This is only applicable when there are more than 1000 transcripts. |
minFiveUTR |
(integer) minimum bp for 5' UTR during filtering for the transcripts. Set to NULL if no 5' UTRs exists for annotation. |
minCDS |
(integer) minimum bp for CDS during filtering for the transcripts |
minThreeUTR |
(integer) minimum bp for 3' UTR during filtering for the transcripts. Set to NULL if no 3' UTRs exists for annotation. |
firstN |
(integer) Represents how many bases of the transcripts downstream of start codons to use for initial estimation of the periodicity. |
min_reads |
default (1000), how many reads must a read-length have to be considered for periodicity. |
accepted.lengths |
accepted readlengths, default 1:1000, usually ribo-seq is between 26:34. |
output_format |
default (bed), use export.bed or ORFik optimized
(bedo) using |
For more details, see: detectRibosomeShifts
NULL (Objects are saved to out.dir/pshited/"name_pshifted.bed" or .bedo)
Other pshifting:
changePointAnalysis(),
detectRibosomeShifts(),
shiftFootprints()