Convenience Functions

Overview

Certain functions have been included in pmartR to simplify the user’s experience by allowing them to retrieve information stored in attributes of the omicsData object. We’ll demonstrate these functions with some of the example omicsData objects from the pmartRdata package.

library(pmartR)
library(pmartRdata)
mypro <- pro_object
mymetab <- metab_object
mynmr <- nmr_identified_object

get_data_class() - Returns data_class attribute from statRes or trellData object, inherited from the omicsData used in imd_anova() or format_data()

# get a statRes object using the proData object
mypro <- group_designation(omicsData = mypro, main_effects = "Phenotype")
myfilter <- imdanova_filter(omicsData = mypro)
mypro <- applyFilt(filter_object = myfilter, omicsData = mypro, min_nonmiss_anova = 2, min_nonmiss_gtest = 3)

## You have specified remove_singleton_groups = TRUE, but there are no singleton groups to remove. Proceeding with application of the IMD-ANOVA filter.

mystats <- imd_anova(omicsData = mypro, test_method = "combined")

## Joining with `by = join_by(SampleID)`

## Joining with `by = join_by(RazorProtein)`

get_data_class(mystats)

## [1] "proData"

get_data_info() - Returns a list containing the data scale, normalization information, number of unique entries in e_data, number of missing observations in e_data, proportion of missing observations in e_data, number of samples, and data type

get_data_info(omicsData = mypro)

## $data_scale_orig
## [1] "abundance"
## 
## $data_scale
## [1] "log2"
## 
## $norm_info
## $norm_info$is_normalized
## [1] TRUE
## 
## 
## $num_edata
## [1] 2737
## 
## $num_miss_obs
## [1] 13855
## 
## $prop_missing
## [1] 0.2109213
## 
## $num_samps
## [1] 24
## 
## $data_types
## NULL
## 
## $batch_info
## $batch_info$is_bc
## [1] FALSE

get_data_scale() - Returns current data scale which may be different from the original data scale (if edata_transform() was used)

get_data_scale(omicsObject = mypro)

## [1] "log2"

get_data_scale(omicsObject = mymetab)

## [1] "abundance"

get_data_scale(omicsObject = mynmr)

## [1] "abundance"

get_data_scale_orig() - Retrieves the character string indicating the scale the data was originally on when the omicsData object was created

get_data_scale_orig(omicsObject = mypro)

## [1] "abundance"

get_data_scale_orig(omicsObject = mymetab)

## [1] "abundance"

get_data_scale_orig(omicsObject = mynmr)

## [1] "abundance"

get_edata_cname() - Returns the name of the column in e_data that contains the biomolecule IDs

get_edata_cname(omicsObject = mypro)

## [1] "RazorProtein"

get_edata_cname(omicsObject = mymetab)

## [1] "Metabolite"

get_edata_cname(omicsObject = mynmr)

## [1] "Metabolite"

get_emeta_cname() - Returns the name of the column in e_meta that contains the mapping to biomolecules in e_data

get_emeta_cname(omicsObject = mypro)

## [1] "RazorProtein"

get_emeta_cname(omicsObject = mymetab)

## NULL

get_emeta_cname(omicsObject = mynmr)

## [1] "Metabolite"

get_fdata_cname() - Returns the name of the column in f_data that contains the names of the samples

get_fdata_cname(omicsObject = mypro)

## [1] "SampleID"

get_fdata_cname(omicsObject = mymetab)

## [1] "SampleID"

get_fdata_cname(omicsObject = mynmr)

## [1] "SampleID"

get_group_DF() - A data.frame with columns for sample ID and group. If two main effects are provided, the original main effect levels for each sample are returned as the third and fourth columns of the data frame. Additionally, the covariates provided will be listed as attributes of this data frame. For both mymetab and mynmr, we have not designated groups yet so the results are NULL.

get_group_DF(omicsData = mypro)

##                  SampleID      Group
## 1  Sample_20_Phenotype3_A Phenotype3
## 2  Sample_33_Phenotype3_A Phenotype3
## 3  Sample_49_Phenotype3_A Phenotype3
## 4  Sample_47_Phenotype3_A Phenotype3
## 5  Sample_50_Phenotype3_B Phenotype3
## 6  Sample_36_Phenotype3_B Phenotype3
## 7   Sample_2_Phenotype3_B Phenotype3
## 8  Sample_34_Phenotype3_B Phenotype3
## 9  Sample_41_Phenotype1_A Phenotype1
## 10 Sample_22_Phenotype1_A Phenotype1
## 11 Sample_46_Phenotype1_A Phenotype1
## 12 Sample_27_Phenotype1_A Phenotype1
## 13  Sample_7_Phenotype1_B Phenotype1
## 14 Sample_19_Phenotype1_B Phenotype1
## 15 Sample_37_Phenotype1_B Phenotype1
## 16 Sample_31_Phenotype1_B Phenotype1
## 17  Sample_3_Phenotype2_A Phenotype2
## 18 Sample_38_Phenotype2_A Phenotype2
## 19 Sample_15_Phenotype2_A Phenotype2
## 20 Sample_35_Phenotype2_A Phenotype2
## 21 Sample_44_Phenotype2_B Phenotype2
## 22  Sample_6_Phenotype2_B Phenotype2
## 23 Sample_12_Phenotype2_B Phenotype2
## 24  Sample_9_Phenotype2_B Phenotype2

get_group_DF(omicsData = mymetab)

## NULL

get_group_DF(omicsData = mynmr)

## NULL

get_group_table() - This function returns a table with number of samples per group

get_group_table(omicsObject = mypro)

## group
## Phenotype1 Phenotype2 Phenotype3 
##          8          8          8

get_isobaric_info() - A list containing the following six elements: exp_cname, channel_cname, refpool_channel, refpool_cname, refpool_notation, and norm_info (list containing a single logical element that indicates whether the data have been normalized to a reference pool

myiso <- edata_transform(omicsData = isobaric_object, data_scale = "log2")
myiso_normalized <- normalize_isobaric(
  omicsData = myiso,
  exp_cname = "Plex",
  apply_norm = TRUE,
  refpool_cname = "Virus",
  refpool_notation = "Pool"
)
get_isobaric_info(omicsData = myiso_normalized)

## $exp_cname
## [1] "Plex"
## 
## $channel_cname
## NULL
## 
## $refpool_channel
## NULL
## 
## $refpool_cname
## [1] "Virus"
## 
## $refpool_notation
## [1] "Pool"
## 
## $norm_info
## $norm_info$is_normalized
## [1] TRUE

get_meta_info() - Retrieves the values in the meta_info attribute from an omicsData object

get_meta_info(omicsData = mynmr)

## $meta_data
## [1] TRUE
## 
## $num_emeta
## [1] 38

get_nmr_info() - A list containing the following three elements: metabolite_name, sample_property_cname, and norm_info (list containing two logical elements that indicate i) whether the data have been normalized to a spiked in metabolite or to a property taking sample-specific values and ii) whether the data have been back transformed so the values are on a similar scale to the raw values before normalization.

get_nmr_info(omicsData = mynmr)

## $metabolite_name
## [1] NA
## 
## $sample_property_cname
## [1] NA
## 
## $norm_info
## $norm_info$is_normalized
## [1] FALSE
## 
## $norm_info$backtransform
## [1] NA

mynmr <- edata_transform(
  omicsData = nmr_identified_object,
  data_scale = "log2"
)

# Normalization using a "spiked in" metabolite
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  metabolite_name = "unkm1.53",
  backtransform = TRUE
)
get_nmr_info(omicsData = nmr_norm)

## $metabolite_name
## [1] "unkm1.53"
## 
## $sample_property_cname
## NULL
## 
## $norm_info
## $norm_info$is_normalized
## [1] TRUE
## 
## $norm_info$backtransform
## [1] TRUE
## 
## $norm_info$norm_method
## [1] "nmrObject was normalized using metabolite_name: unkm1.53"
## 
## $norm_info$norm_params
##  [1] 4.363716 4.779691 5.517468 4.510298 4.605259 5.284030 5.943928 6.534026
##  [9] 5.634490 5.458099 5.762838 5.638715 5.403021 5.889520 6.261542 5.640842
## [17] 4.228711 5.819901 6.482046 4.510938 6.531002 5.143085 4.295073 5.201547
## [25] 3.969331 4.707095 4.120682 4.794893 6.439716 6.050808 5.967296 6.467480
## [33] 5.859282 6.098328 6.600868 4.365027 6.036377 4.347367 5.047161 6.189109
## [41] 5.005238

# Normalization using a sample property
nmr_norm <- normalize_nmr(
  omicsData = mynmr, apply_norm = TRUE,
  sample_property_cname = "Concentration",
  backtransform = TRUE
)
get_nmr_info(omicsData = nmr_norm)

## $metabolite_name
## NULL
## 
## $sample_property_cname
## [1] "Concentration"
## 
## $norm_info
## $norm_info$is_normalized
## [1] TRUE
## 
## $norm_info$backtransform
## [1] TRUE
## 
## $norm_info$norm_method
## [1] "nmrObject was normalized using sample property: Concentration"
## 
## $norm_info$norm_params
##  [1] 5.697732 5.374048 4.877954 5.322915 5.301788 5.098320 4.498749 4.838841
##  [9] 5.311861 5.010194 5.680948 4.958344 5.342242 5.807285 4.887392 4.875128
## [17] 4.757206 5.515011 5.638298 5.602582 5.471601 5.259434 5.353657 5.216526
## [25] 5.639881 5.531923 5.232129 5.584298 5.048396 5.273855 5.564034 5.649313
## [33] 5.869584 5.840797 5.113072 5.768750 5.266933 5.659354 5.290421 5.258544
## [41] 5.301627

get_filters() - A list containing filter class objects. Each element in this list corresponds to a filter applied to the data, and filters are listed in the order they were applied.

get_filters(omicsData = mypro)

## [[1]]
## $type
## [1] "imdanovaFilt"
## 
## $threshold
##   min_nonmiss_anova min_nonmiss_gtest
## 1                 2                 3
## 
## $filtered
##   [1] "sp|Q99567|NUP88_HUMAN"     "sp|Q8N668|COMD1_HUMAN"    
##   [3] "sp|Q96AX1|VP33A_HUMAN"     "sp|Q86SZ2|TPC6B_HUMAN"    
##   [5] "sp|Q9H008|LHPP_HUMAN"      "sp|P19634|SL9A1_HUMAN"    
##   [7] "sp|Q969N2|PIGT_HUMAN"      "sp|P16278|BGAL_HUMAN"     
##   [9] "sp|O15321|TM9S1_HUMAN"     "sp|O75935|DCTN3_HUMAN"    
##  [11] "sp|P61221|ABCE1_HUMAN"     "sp|P09455|RET1_HUMAN"     
##  [13] "sp|Q15345|LRC41_HUMAN"     "sp|Q00653|NFKB2_HUMAN"    
##  [15] "sp|Q5K4L6|S27A3_HUMAN"     "sp|P20591|MX1_HUMAN"      
##  [17] "sp|Q96SK2|TM209_HUMAN"     "sp|O15049|N4BP3_HUMAN"    
##  [19] "sp|O75167|PHAR2_HUMAN"     "sp|P59768|GBG2_HUMAN"     
##  [21] "sp|Q9UEU0|VTI1B_HUMAN"     "sp|Q9HCU5|PREB_HUMAN"     
##  [23] "sp|Q99615|DNJC7_HUMAN"     "sp|Q969X1|LFG3_HUMAN"     
##  [25] "sp|P54725|RD23A_HUMAN"     "sp|Q9NY33|DPP3_HUMAN"     
##  [27] "sp|P35542|SAA4_HUMAN"      "sp|P83916|CBX1_HUMAN"     
##  [29] "sp|Q86W92|LIPB1_HUMAN"     "sp|Q8NI22|MCFD2_HUMAN"    
##  [31] "sp|O96013|PAK4_HUMAN"      "sp|Q63HQ2|EGFLA_HUMAN"    
##  [33] "sp|Q8NF37|PCAT1_HUMAN"     "sp|O76031|CLPX_HUMAN"     
##  [35] "sp|Q13523|PRP4B_HUMAN"     "sp|O95169|NDUB8_HUMAN"    
##  [37] "sp|Q9Y315|DEOC_HUMAN"      "sp|P17693|HLAG_HUMAN"     
##  [39] "sp|Q9H4G4|GAPR1_HUMAN"     "sp|Q8N6T3|ARFG1_HUMAN"    
##  [41] "sp|P32320|CDD_HUMAN"       "sp|Q9BQE5|APOL2_HUMAN"    
##  [43] "sp|Q9H3N8|HRH4_HUMAN"      "sp|Q7L804|RFIP2_HUMAN"    
##  [45] "sp|Q9BV79|MECR_HUMAN"      "sp|Q8N335|GPD1L_HUMAN"    
##  [47] "sp|O43246|CTR4_HUMAN"      "sp|Q86UE4|LYRIC_HUMAN"    
##  [49] "sp|Q9BYX4|IFIH1_HUMAN"     "sp|O43181|NDUS4_HUMAN"    
##  [51] "sp|Q6FI81|CPIN1_HUMAN"     "sp|Q9Y673|ALG5_HUMAN"     
##  [53] "sp|Q9BY77|PDIP3_HUMAN"     "sp|P28329|CLAT_HUMAN"     
##  [55] "sp|Q8IY26|PLPP6_HUMAN"     "sp|P55287|CAD11_HUMAN"    
##  [57] "sp|O43699|SIGL6_HUMAN"     "sp|Q8N1B4|VPS52_HUMAN"    
##  [59] "sp|O95202|LETM1_HUMAN"     "sp|Q07283|TRHY_HUMAN"     
##  [61] "sp|O14874|BCKD_HUMAN"      "sp|P15502|ELN_HUMAN"      
##  [63] "sp|Q9H6U8|ALG9_HUMAN"      "sp|Q15555|MARE2_HUMAN"    
##  [65] "sp|P10915|HPLN1_HUMAN"     "sp|Q659C4|LAR1B_HUMAN"    
##  [67] "sp|Q8WVQ1|CANT1_HUMAN"     "sp|P24928|RPB1_HUMAN"     
##  [69] "sp|O14925|TIM23_HUMAN"     "sp|Q9UHL4|DPP2_HUMAN"     
##  [71] "sp|Q8N0X7|SPART_HUMAN"     "sp|P14735|IDE_HUMAN"      
##  [73] "sp|O14618|CCS_HUMAN"       "sp|Q8N357|S35F6_HUMAN"    
##  [75] "sp|P23297|S10A1_HUMAN"     "sp|P09972|ALDOC_HUMAN"    
##  [77] "sp|Q5VW32|BROX_HUMAN"      "sp|Q8N6M0|OTU6B_HUMAN"    
##  [79] "sp|P62745|RHOB_HUMAN"      "sp|Q8IY63|AMOL1_HUMAN"    
##  [81] "sp|P48960|CD97_HUMAN"      "sp|Q9NRN7|ADPPT_HUMAN"    
##  [83] "sp|Q9H2V7|SPNS1_HUMAN"     "sp|Q04941|PLP2_HUMAN"     
##  [85] "sp|Q8WVJ2|NUDC2_HUMAN"     "sp|P30405|PPIF_HUMAN"     
##  [87] "sp|Q14694|UBP10_HUMAN"     "sp|Q5JRX3|PREP_HUMAN"     
##  [89] "sp|Q7Z5K2|WAPL_HUMAN"      "sp|P12694|ODBA_HUMAN"     
##  [91] "sp|P52701|MSH6_HUMAN"      "sp|Q9H9A5|CNO10_HUMAN"    
##  [93] "sp|Q12841|FSTL1_HUMAN"     "sp|Q9BTT0|AN32E_HUMAN"    
##  [95] "sp|Q9BVA1|TBB2B_HUMAN"     "sp|O60760|HPGDS_HUMAN"    
##  [97] "sp|P01242|SOM2_HUMAN"      "sp|Q8N3U4|STAG2_HUMAN"    
##  [99] "sp|P09488|GSTM1_HUMAN"     "sp|P48553|TPC10_HUMAN"    
## [101] "sp|Q16718|NDUA5_HUMAN"     "sp|P19623|SPEE_HUMAN"     
## [103] "sp|Q9Y646|CBPQ_HUMAN"      "sp|P30837|AL1B1_HUMAN"    
## [105] "sp|P15153|RAC2_HUMAN"      "sp|Q5T5P2|SKT_HUMAN"      
## [107] "sp|Q9UN36|NDRG2_HUMAN"     "sp|P63218|GBG5_HUMAN"     
## [109] "sp|P39880|CUX1_HUMAN"      "sp|Q15036|SNX17_HUMAN"    
## [111] "sp|Q9Y281|COF2_HUMAN"      "sp|Q6ZUJ8|BCAP_HUMAN"     
## [113] "sp|Q9UIL1|SCOC_HUMAN"      "sp|Q5JU69|TOR2A_HUMAN"    
## [115] "sp|P14598|NCF1_HUMAN"      "sp|Q6ZMZ3|SYNE3_HUMAN"    
## [117] "sp|O95671|ASML_HUMAN"      "sp|Q99836|MYD88_HUMAN"    
## [119] "sp|Q9H583|HEAT1_HUMAN"     "sp|Q16787|LAMA3_HUMAN"    
## [121] "sp|A0A0C4DH67|KV108_HUMAN" "sp|P01594|KV133_HUMAN"    
## [123] "sp|P25205|MCM3_HUMAN"      "sp|Q96KG9|SCYL1_HUMAN"    
## [125] "sp|P01704|LV214_HUMAN"     "sp|Q06136|KDSR_HUMAN"     
## [127] "sp|P54753|EPHB3_HUMAN"     "sp|Q96CM8|ACSF2_HUMAN"    
## [129] "sp|Q6UY01|LRC31_HUMAN"     "sp|Q9UPQ0|LIMC1_HUMAN"    
## [131] "sp|Q9Y6R7|FCGBP_HUMAN"     "sp|P78524|ST5_HUMAN"      
## [133] "sp|O95786|DDX58_HUMAN"     "sp|O95182|NDUA7_HUMAN"    
## [135] "sp|P54105|ICLN_HUMAN"      "sp|Q13123|RED_HUMAN"      
## [137] "sp|Q9UEY8|ADDG_HUMAN"      "sp|Q15126|PMVK_HUMAN"     
## [139] "sp|Q9UBN7|HDAC6_HUMAN"     "sp|P61086|UBE2K_HUMAN"    
## [141] "sp|Q96T37|RBM15_HUMAN"     "sp|Q9HD42|CHM1A_HUMAN"    
## [143] "sp|Q96B23|CR025_HUMAN"     "sp|Q5JVF3|PCID2_HUMAN"    
## [145] "sp|Q01813|PFKAP_HUMAN"     "sp|O75208|COQ9_HUMAN"     
## [147] "sp|Q9Y4W2|LAS1L_HUMAN"     "sp|Q16539|MK14_HUMAN"     
## [149] "sp|Q9P0S3|ORML1_HUMAN"     "sp|Q9C010|IPKB_HUMAN"     
## [151] "sp|Q12768|WASC5_HUMAN"     "sp|Q96CM3|RUSD4_HUMAN"    
## [153] "sp|O75521|ECI2_HUMAN"      "sp|P14854|CX6B1_HUMAN"    
## [155] "sp|P51398|RT29_HUMAN"      "sp|P0DI82|TPC2B_HUMAN"    
## [157] "sp|Q14914|PTGR1_HUMAN"     "sp|P01903|DRA_HUMAN"      
## [159] "sp|P62491|RB11A_HUMAN"     "sp|P52756|RBM5_HUMAN"     
## [161] "sp|O43172|PRP4_HUMAN"      "sp|P45973|CBX5_HUMAN"     
## [163] "sp|Q9UBD5|ORC3_HUMAN"      "sp|Q9NQP4|PFD4_HUMAN"     
## [165] "sp|O75569|PRKRA_HUMAN"     "sp|Q9UQ72|PSG11_HUMAN"    
## [167] "sp|Q96Q11|TRNT1_HUMAN"     "sp|Q9Y2L1|RRP44_HUMAN"    
## [169] "sp|P52815|RM12_HUMAN"      "sp|P09486|SPRC_HUMAN"     
## [171] "sp|Q14061|COX17_HUMAN"     "sp|Q96K17|BT3L4_HUMAN"    
## [173] "sp|Q09472|EP300_HUMAN"     "sp|Q9NTX5|ECHD1_HUMAN"    
## [175] "sp|Q8NEU8|DP13B_HUMAN"     "sp|Q9UBW8|CSN7A_HUMAN"    
## [177] "sp|P11217|PYGM_HUMAN"      "sp|Q59GN2|R39L5_HUMAN"    
## [179] "sp|Q7Z5L9|I2BP2_HUMAN"     "sp|Q96NY8|NECT4_HUMAN"    
## [181] "sp|Q14134|TRI29_HUMAN"     "sp|Q8IYI6|EXOC8_HUMAN"    
## [183] "sp|O75122|CLAP2_HUMAN"     "sp|Q86UY8|NT5D3_HUMAN"    
## [185] "sp|P0DJI9|SAA2_HUMAN"      "sp|Q14444|CAPR1_HUMAN"    
## [187] "sp|P27449|VATL_HUMAN"      "sp|Q16706|MA2A1_HUMAN"    
## [189] "sp|Q08752|PPID_HUMAN"      "sp|P07919|QCR6_HUMAN"     
## [191] "sp|Q8NFF5|FAD1_HUMAN"      "sp|Q58FF6|H90B4_HUMAN"    
## [193] "sp|Q9Y6K0|CEPT1_HUMAN"     "sp|Q13620|CUL4B_HUMAN"    
## [195] "sp|P07360|CO8G_HUMAN"      "sp|Q96PE2|ARHGH_HUMAN"    
## [197] "sp|Q9NYF0|DACT1_HUMAN"     "sp|Q9H7D0|DOCK5_HUMAN"    
## [199] "sp|P19878|NCF2_HUMAN"      "sp|Q8IY67|RAVR1_HUMAN"    
## [201] "sp|O75448|MED24_HUMAN"     "sp|Q08495|DEMA_HUMAN"     
## [203] "sp|Q9BUR5|MIC26_HUMAN"     "sp|Q15785|TOM34_HUMAN"    
## [205] "sp|Q96EY7|PTCD3_HUMAN"     "sp|O43236|SEPT4_HUMAN"    
## [207] "sp|Q8TBA6|GOGA5_HUMAN"     "sp|O43464|HTRA2_HUMAN"    
## [209] "sp|O96019|ACL6A_HUMAN"     "sp|Q9Y263|PLAP_HUMAN"     
## [211] "sp|P22830|HEMH_HUMAN"      "sp|Q9NVP1|DDX18_HUMAN"    
## [213] "sp|P48507|GSH0_HUMAN"      "sp|P10415|BCL2_HUMAN"     
## [215] "sp|Q6ZSR9|YJ005_HUMAN"     "sp|O14498|ISLR_HUMAN"     
## [217] "sp|Q9Y279|VSIG4_HUMAN"     "sp|Q5VW38|GP107_HUMAN"    
## [219] "sp|Q9HCJ6|VAT1L_HUMAN"     "sp|P62834|RAP1A_HUMAN"    
## [221] "sp|P15151|PVR_HUMAN"       "sp|Q8N4V1|MMGT1_HUMAN"    
## [223] "sp|Q8IUR0|TPPC5_HUMAN"     "sp|Q9NUQ2|PLCE_HUMAN"     
## [225] "sp|P63172|DYLT1_HUMAN"     "sp|P51689|ARSD_HUMAN"     
## [227] "sp|Q86VR2|RETR3_HUMAN"     "sp|P13598|ICAM2_HUMAN"    
## [229] "sp|P0DMP2|SRG2B_HUMAN"     "sp|O14929|HAT1_HUMAN"     
## [231] "sp|Q9Y580|RBM7_HUMAN"      "sp|Q6UXN9|WDR82_HUMAN"    
## [233] "sp|Q96SL4|GPX7_HUMAN"      "sp|Q9H2M9|RBGPR_HUMAN"    
## [235] "sp|P22748|CAH4_HUMAN"      "sp|P09234|RU1C_HUMAN"     
## [237] "sp|Q9BU23|LMF2_HUMAN"      "sp|O43678|NDUA2_HUMAN"    
## [239] "sp|Q08174|PCDH1_HUMAN"     "sp|P82675|RT05_HUMAN"     
## [241] "sp|O75746|CMC1_HUMAN"      "sp|O95155|UBE4B_HUMAN"    
## [243] "sp|O43292|GPAA1_HUMAN"     "sp|Q9BXJ9|NAA15_HUMAN"    
## [245] "sp|Q9C0D9|EPT1_HUMAN"     
## 
## $method
## [1] "combined"
## 
## attr(,"class")
## [1] "filter"

get_data_norm() - Returns the norm_info element of the data_info attribute indicating whether the data have been normalized

get_data_norm(omicsObject = mypro)

## [1] TRUE

get_data_norm(omicsObject = mymetab)

## [1] FALSE

get_data_norm(omicsObject = mynmr)

## [1] FALSE

get_isobaric_norm() - A logical value indicating whether the data have been isobaric normalized

get_isobaric_norm(myiso)

## [1] FALSE

get_isobaric_norm(myiso_normalized)

## [1] TRUE

get_nmr_norm() - A logical value indicating whether the data have been NMR normalized

get_nmr_norm(omicsData = mynmr)

## [1] FALSE

get_nmr_norm(omicsData = nmr_norm)

## [1] TRUE

get_comparisons() - Returns a data frame with comparisons and their indices

imd_anova_res <- imd_anova(
  omicsData = mypro,
  test_method = "comb",
  pval_adjust_a_multcomp = "bon",
  pval_adjust_g_multcomp = "bon"
)

## Joining with `by = join_by(SampleID)`
## Joining with `by = join_by(RazorProtein)`

get_comparisons(compObj = imd_anova_res)

##                comparisons index
## 1 Phenotype3_vs_Phenotype1     1
## 2 Phenotype3_vs_Phenotype2     2
## 3 Phenotype1_vs_Phenotype2     3

Kelly Stratton, Lisa Bramer

2024-02-28

Overview

References

Convenience Functions

Kelly Stratton, Lisa Bramer

2024-02-28

Overview

Related to Data Structure or Setup

Related to Filters

Related to Normalization

Related to Statistical Comparisons

References