signal_at_orf_se: Signal around ORF start or end positions
In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description Usage Arguments Value Examples

This function allows you to pull out the ChIP signal around the translation start or end for all ORFs in the genome. It collects the signal between specified extensions up and downstream of the chosen ORF limit.
The function takes as input the wiggle data as a list of 16 chromosomes. (output of readall_tab).

Note: Our wiggle data always contains gaps with missing chromosome coordinates and ChIP-seq signal. The way this function deals with that is by skipping affected genes. The number of skipped genes in each chromosome is printed to the console, as well as the final count (and percentage) of skipped genes.

1 2	signal_at_orf_se(inputData, gff, gffFile, limit = "start", upstrExt = 500, downstrExt = 1500, saveFile = FALSE)

`inputData`	As a list of the 16 chr wiggle data (output of `readall_tab`). No default.
`gff`	Optional dataframe of the gff providing the ORF cordinates. Must be provided if `gffFile` is not. No default. Note: You can use the function `gff_read` in hwglabr to load your selected gff file.
`gffFile`	Optional string indicating path to the gff file providing the ORF cordinates. Must be provided if `gff` is not. No default.
`limit`	String indicating whether to use translation start or end as a the reference point. Accepts one of `start` or `end`. Defaults to `start`.
`upstrExt`	Number specifying the extension in bp to collect upstream of the reference limit. Defaults to `500`.
`downstrExt`	Number specifying the extension in bp to collect downstream of the reference limit. Defaults to `1500`.
`saveFile`	Boolean indicating whether output should be written to a .txt file (in current working directory). If `saveFile = FALSE`, output is returned to screen or an R object (if assigned). Defaults to `FALSE`.

A local data frame with four columns:

chr Chromosome number
position Nucleotide coordinate (in normalized total length of 1 kb)
signal ChIP-seq signal at each position (1 to 1000)
gene Systematic gene name

## Not run: 
signal_at_orf_se(WT, gff = gff)

signal_at_orf_se(WT, gffFile = S288C_annotation_modified.gff, limit = 'end',
                 upstrExt = 1500, downstrExt = 500, saveFile = TRUE)

## End(Not run)