Add or update "is_outlier" column in the "nacho" field of an object from
a call to load_rcc() or normalise() (nacho_object$nacho),
using the current quality-control thresholds.
Arguments
- nacho_object
[list] A list object of class
"nacho"obtained fromload_rcc()ornormalise().
Value
A [list] object of class "nacho".
Examples
data(GSE74821)
nacho_object <- check_outliers(GSE74821)
head(nacho_object$nacho)
#> Key: <IDFILE>
#> IDFILE
#> <char>
#> 1: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 2: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 3: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 4: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 5: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 6: GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> file_path
#> <char>
#> 1: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 2: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 3: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 4: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 5: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 6: /private/var/folders/gn/mxv05rj52wd1yg1hb018s4s40000gn/T/RtmpnCdvu5/GSE74821/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> title geo_accession status submission_date
#> <char> <char> <char> <char>
#> 1: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> 2: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> 3: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> 4: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> 5: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> 6: LGWU101986-1036378WU GSM1934697 Public on Nov 10 2015 Nov 09 2015
#> last_update_date type channel_count source_name_ch1 organism_ch1
#> <char> <char> <char> <char> <char>
#> 1: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> 2: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> 3: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> 4: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> 5: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> 6: Nov 10 2015 RNA 1 Breast Tumor CALGB 101986 Homo sapiens
#> characteristics_ch1 characteristics_ch1.1
#> <char> <char>
#> 1: gender: female tissue type: Breast Tumor
#> 2: gender: female tissue type: Breast Tumor
#> 3: gender: female tissue type: Breast Tumor
#> 4: gender: female tissue type: Breast Tumor
#> 5: gender: female tissue type: Breast Tumor
#> 6: gender: female tissue type: Breast Tumor
#> characteristics_ch1.2 biomaterial_provider_ch1
#> <char> <char>
#> 1: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> 2: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> 3: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> 4: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> 5: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> 6: fixative: Formalin-Fixed Paraffin Embedded Tissue CALGB
#> treatment_protocol_ch1 growth_protocol_ch1 molecule_ch1
#> <char> <char> <char>
#> 1: <NA> N/A total RNA
#> 2: <NA> N/A total RNA
#> 3: <NA> N/A total RNA
#> 4: <NA> N/A total RNA
#> 5: <NA> N/A total RNA
#> 6: <NA> N/A total RNA
#> extract_protocol_ch1
#> <char>
#> 1: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> 2: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> 3: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> 4: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> 5: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> 6: http://www.nanostring.com/media/pdf/TN_Using_nCounter_with_FFPE_Samples.pdf
#> label_ch1 label_protocol_ch1 taxid_ch1 hyb_protocol scan_protocol
#> <char> <char> <char> <char> <char>
#> 1: NA <NA> 9606 <NA> <NA>
#> 2: NA <NA> 9606 <NA> <NA>
#> 3: NA <NA> 9606 <NA> <NA>
#> 4: NA <NA> 9606 <NA> <NA>
#> 5: NA <NA> 9606 <NA> <NA>
#> 6: NA <NA> 9606 <NA> <NA>
#> data_processing platform_id contact_name contact_email contact_phone
#> <char> <char> <char> <char> <char>
#> 1: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> 2: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> 3: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> 4: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> 5: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> 6: <NA> GPL21114 Sherri,R,Davies daviess@wustl.edu 3147473073
#> contact_institute contact_address contact_city contact_state
#> <char> <char> <char> <char>
#> 1: Washington University 4950 Parkview Place Saint Louis MO
#> 2: Washington University 4950 Parkview Place Saint Louis MO
#> 3: Washington University 4950 Parkview Place Saint Louis MO
#> 4: Washington University 4950 Parkview Place Saint Louis MO
#> 5: Washington University 4950 Parkview Place Saint Louis MO
#> 6: Washington University 4950 Parkview Place Saint Louis MO
#> contact_zip/postal_code contact_country
#> <char> <char>
#> 1: 63110 USA
#> 2: 63110 USA
#> 3: 63110 USA
#> 4: 63110 USA
#> 5: 63110 USA
#> 6: 63110 USA
#> supplementary_file
#> <char>
#> 1: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 2: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 3: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 4: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 5: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 6: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1934nnn/GSM1934697/suppl/GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> data_row_count fixative:ch1 gender:ch1
#> <char> <char> <char>
#> 1: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> 2: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> 3: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> 4: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> 5: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> 6: 72 Formalin-Fixed Paraffin Embedded Tissue female
#> tissue type:ch1 Header.header_FileVersion Header.header_SoftwareVersion
#> <char> <char> <char>
#> 1: Breast Tumor 1.6 2.1.1.0005
#> 2: Breast Tumor 1.6 2.1.1.0005
#> 3: Breast Tumor 1.6 2.1.1.0005
#> 4: Breast Tumor 1.6 2.1.1.0005
#> 5: Breast Tumor 1.6 2.1.1.0005
#> 6: Breast Tumor 1.6 2.1.1.0005
#> Sample_Attributes.sample_ID Sample_Attributes.sample_Owner
#> <char> <char>
#> 1: LGWU101986-1036378WU palldred
#> 2: LGWU101986-1036378WU palldred
#> 3: LGWU101986-1036378WU palldred
#> 4: LGWU101986-1036378WU palldred
#> 5: LGWU101986-1036378WU palldred
#> 6: LGWU101986-1036378WU palldred
#> Sample_Attributes.sample_Comments Sample_Attributes.sample_Date
#> <char> <char>
#> 1: 250 ng input 20111102
#> 2: 250 ng input 20111102
#> 3: 250 ng input 20111102
#> 4: 250 ng input 20111102
#> 5: 250 ng input 20111102
#> 6: 250 ng input 20111102
#> Sample_Attributes.sample_GeneRLF Sample_Attributes.sample_SystemAPF
#> <char> <char>
#> 1: RUO PAM50 C941 n6_vDV1
#> 2: RUO PAM50 C941 n6_vDV1
#> 3: RUO PAM50 C941 n6_vDV1
#> 4: RUO PAM50 C941 n6_vDV1
#> 5: RUO PAM50 C941 n6_vDV1
#> 6: RUO PAM50 C941 n6_vDV1
#> Lane_Attributes.lane_ID Lane_Attributes.lane_FovCount
#> <char> <char>
#> 1: 2 1155
#> 2: 2 1155
#> 3: 2 1155
#> 4: 2 1155
#> 5: 2 1155
#> 6: 2 1155
#> Lane_Attributes.lane_FovCounted Lane_Attributes.lane_ScannerID
#> <char> <char>
#> 1: 1155 DA26
#> 2: 1155 DA26
#> 3: 1155 DA26
#> 4: 1155 DA26
#> 5: 1155 DA26
#> 6: 1155 DA26
#> Lane_Attributes.lane_StagePosition Lane_Attributes.lane_BindingDensity
#> <char> <char>
#> 1: 1 0.30
#> 2: 1 0.30
#> 3: 1 0.30
#> 4: 1 0.30
#> 5: 1 0.30
#> 6: 1 0.30
#> Lane_Attributes.lane_CartridgeID Messages CodeClass Name Accession
#> <char> <char> <char> <char> <char>
#> 1: 20111102-9741-1 NULL Endogenous FOXA1 NM_004496.2
#> 2: 20111102-9741-1 NULL Endogenous EXO1 NM_006027.3
#> 3: 20111102-9741-1 NULL Endogenous CDH3 NM_001793.3
#> 4: 20111102-9741-1 NULL Endogenous BIRC5 NM_001168.2
#> 5: 20111102-9741-1 NULL Endogenous MKI67 NM_002417.2
#> 6: 20111102-9741-1 NULL Endogenous CCNE1 NM_001238.1
#> Count Date ID BD ScannerID StagePosition CartridgeID FoV
#> <int> <char> <char> <num> <char> <char> <char> <num>
#> 1: 2845 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> 2: 388 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> 3: 115 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> 4: 682 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> 5: 775 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> 6: 342 20111102 2 0.3 DA26 1 20111102-9741-1 100
#> PCL LoD MC MedC PC01 PC02 PC03 PC04 PC05
#> <num> <num> <num> <num> <num> <num> <num> <num> <num>
#> 1: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> 2: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> 3: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> 4: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> 5: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> 6: 0.98857 15.46 2049.32 672 1.18781 4.599829 -1.525226 -2.133031 0.4390433
#> PC06 PC07 PC08 PC09 PC10 Positive_factor
#> <num> <num> <num> <num> <num> <num>
#> 1: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> 2: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> 3: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> 4: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> 5: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> 6: -1.422065 2.353212 -1.186074 0.03486358 -0.2710683 0.8074219
#> Negative_factor House_factor is_outlier Count_Norm
#> <num> <num> <lgcl> <num>
#> 1: 16.28558 0.6221572 FALSE 1421
#> 2: 16.28558 0.6221572 FALSE 187
#> 3: 16.28558 0.6221572 FALSE 50
#> 4: 16.28558 0.6221572 FALSE 334
#> 5: 16.28558 0.6221572 FALSE 381
#> 6: 16.28558 0.6221572 FALSE 164