Update objects: Objects don't match attributes generated in pmartR as.omicsData calls

[rarichardson92]

I've tried recreating the data objects in this package with pmartR functions, but there are a few differences in attributes that don't match up. Most of these are the inclusion of a techrep_cname in cnames, but there are a few other discrepancies with the pro_object and isobaric_object.

It might also be a good idea to have the check.names = FALSE attribute set for these objects for use in downstream functions.
Discrepancies are detailed in code below:

---

library(pmartR)
library(pmartRdata)

lipid_object2 <- as.lipidData(e_data = lipid_edata, f_data = lipid_fdata, edata_cname = "LipidCommonName", fdata_cname = "Sample_Name", check.names = FALSE)

metab_object2 <- as.metabData(e_data = metab_edata, f_data = metab_fdata, edata_cname = "Metabolite", fdata_cname = "SampleID", check.names = FALSE)

pro_object2 <- as.proData(e_data = pro_edata, f_data = pro_fdata, edata_cname = "Reference", fdata_cname = "SampleID", check.names = FALSE, data_scale = "log2") #  norm_data = TRUE, norm_method = 'median_center' for object

pep_object2 <- as.pepData(e_data = pep_edata, e_meta = pep_emeta, f_data = pep_fdata, edata_cname = "Mass_Tag_ID", fdata_cname = "SampleID", emeta_cname = "Protein", check.names = FALSE)

techrep_pep_object2 <- as.pepData(e_data = techrep_edata, f_data = techrep_fdata, edata_cname = "Mass_Tag_ID", fdata_cname = "RunID", techrep_cname = "TECH_REP", data_scale = "log2")

isobaric_object2 <- as.isobaricpepData(e_data = isobaric_edata, e_meta = isobaric_emeta, f_data = isobaric_fdata, edata_cname = "Peptide", fdata_cname = "Sample", emeta_cname = "Protein", exp_cname = "Set", refpool_cname = "Reference", refpool_notation = "Yes")

#### $techrep_cname == NULL is missing from object, present in object2
all.equal(attributes(lipid_object), attributes(lipid_object2))
attributes(lipid_object)$cnames
attributes(lipid_object2)$cnames

#### $techrep_cname == NULL is missing from object, present in object2
all.equal(attributes(metab_object), attributes(metab_object2))
attributes(metab_object)$cnames
attributes(metab_object2)$cnames

#### $techrep_cname == NULL is missing from object, present in object2
#### $norm_data = TRUE, $norm_method = 'median_center' for object, cannot be set via as.proData
#### Possibly just adjust ?pro_object to notate these differences?
all.equal(attributes(pro_object), attributes(pro_object2))
attributes(pro_object)$cnames
attributes(pro_object2)$cnames

##### Dataframe used to visualize differences
data.frame(unlist(attributes(pro_object)$data_info))
data.frame(unlist(attributes(pro_object2)$data_info))

#### $techrep_cname == NULL is missing from object, present in object2
all.equal(attributes(pep_object), attributes(pep_object2))
attributes(pep_object)$cnames
attributes(pep_object2)$cnames

#### No issues
all.equal(attributes(techrep_pep_object), attributes(techrep_pep_object2))

#### $techrep_cname == NULL is missing from object, present in object2
#### Multiple discrepencies in data_info: $data_norm == FALSE and $isobaric_norm == FALSE for object, norm_info.is_normalized == FALSE for object2. $num_emeta missing from object, despite emeta present. $num_emeta == 500 in object2.
#### $meta_info == FALSE in object despite emeta present, TRUE in object 2
#### $norm_info$is_normalized == FALSE missing from object, present in object2

all.equal(attributes(isobaric_object), attributes(isobaric_object2))
attributes(isobaric_object)$cnames
attributes(isobaric_object2)$cnames

data.frame(unlist(attributes(isobaric_object)$data_info))
data.frame(unlist(attributes(isobaric_object2)$data_info))

attributes(isobaric_object)$meta_info
attributes(isobaric_object2)$meta_info

data.frame(unlist(attributes(isobaric_object)$isobaric_info))
data.frame(unlist(attributes(isobaric_object2)$isobaric_info))