dataframeToRCaMP: Converts a cleaned CSV to an rcamp object.

Description Usage Arguments Details Value

View source: R/main.R


The rcamp object (an S3 object) will hold all the raw data as well as results. This function checks to make sure the following are true:


dataframeToRCaMP(raw_data, time_index = 1, smooth_fxn = FALSE,
  smooth_n = 20, timing_alpha = 2, time_units = "miliseconds",
  time_override = F)



A dataframe containing the data you wish to turn into an experiment object. You are welcome to subset the data before passing it in (ie raw_data[,-c(2,5)] to exclude the second and third column).


The index of the column containing all of the 'Time' data.


A Boolean (default False). Do you want the data, which may or may not be noisy, to be smoothed using a running average. Recommended.


A number to be passed to the running average function. n is the number of points to average at each window. Default is 20.


A number to pass to the timing checker. This alpha is multiplied to the median of the differnces of each time measument. If a time measurment exceeds this threshold, an error is produced. The microscope may have stalled at this point, and furhter investigation is needed to check the data. Default is 2.


* No NA's are contained in the data frame.

* The time_index is assigned correctly, and no timeing errors are detected. Timing errors are defined as gaps in recording that exceed some threshold (defined as the median time multiplied by some alpha).

* There are no extranious intensity values.

The resulting object can be passed to the other funcitons in this program.


An rcamp object.

allgenesconsidered/RCaMP documentation built on May 24, 2019, 3:02 a.m.